Protein interaction networks

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The document discusses protein interaction networks and the STRING database. It describes how STRING uses genomic context, gene fusion, co-expression, and curated data to predict protein-protein interactions. It also explains how STRING integrates this interaction data with chemical compound data to build networks connecting proteins and chemicals. The document provides examples of how STRING can be used to analyze the cell cycle and temporal protein interaction networks, and links to websites for exploring the STRING and STITCH databases.

Technology

Protein interaction networks Lars Juhl Jensen

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In interactome, basically for interaction of proteins there is certain key elements requited, they are: Interactomics and Proteomics, Complementation groups, Modifier screens 1. Interactomics and Proteomics Field of interactomics is concerned with interactions between genes or proteins. They can be genetic interactions, in which two genes are mainly involved in the same functional pathway (leading to a particular phenotype), or physical interactions, in which there is direct physical contact between two proteins (or between protein and DNA) (Janga et al.,2008). 2. Complementation groups Using forward saturation genetics, one may recover several independent mutants with the same (or similar) phenotype (Hernández et al., 2007). There are two possibilities: a) Mutations are in the same gene b) Mutations are in different genes involved in the same pathway. Scenario (b) Can be tested genetically with a complementation test:  Cross two homozygous mutants (samples) and observe heterozygous offspring phenotypes(samples) Mutations in the same gene will not complement  offspring have mutant phenotype Mutations in different genes will complement  offspring have wild Type phenotype  Do pairwise crosses for all mutants to identify complementation groups  Typically each complementation group represents a different gene  If many mutations are recovered in the same genes, this implies saturation

Protein protein interaction

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Proteins facilitates most biological processes in a cell, including gene expression, cell growth, proliferation, nutrient uptake, morphology, motility, intercellular communication and apoptosis. Protein–protein interactions (PPIs) refer to physical contacts established between two or more proteins as a result of biochemical events. These interactions are very important in our lives as any disorder in them can lead to fatal diseases such as Alzheimer’s and Creutzfeld- Jacob Disease. The most well known example of Protein-Protein Interaction is between Actin and Myosin while regulating Muscular contraction in our body. The protein –protein interaction have commonly been termed the ‘INTERACTOME’ by scientists. Homo-Oligomers: Complexes having one type of protein subunits. E.g. : PPIs in Muscle Contraction Hetero-Oligomers: Complexes having multiple types protein subunits. E.g. : PPI between Cytochrome Oxidase and TRPC3 (Transient receptor potential cation channels

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