Building Protein-Protein Interaction Networks with Proteomics and Informatics Tools

Mihaela E. Sardiu, Michael P. Washburn
2011 Journal of Biological Chemistry  
The systematic characterization of the whole interactomes of different model organisms has revealed that the eukaryotic proteome is highly interconnected. Therefore, biological research is progressively shifting away from classical approaches that focus only on a few proteins toward whole protein interaction networks to describe the relationship of proteins in biological processes. In this minireview, we survey the most common methods for the systematic identification of protein interactions
more » ... exemplify different strategies for the generation of protein interaction networks. In particular, we will focus on the recent development of protein interaction networks derived from quantitative proteomics data sets. Global efforts in a variety of model organisms have been conducted or are still under way to understand biological processes or whole organisms at the systems level. Among these, a significant focus is on the elucidation of protein interactions because protein interactions are focal points in almost all cellular processes. Within a cell, protein interactions range from pairwise, as in the case of ligand-receptor binding during signal transduction, to the formation of macromolecular protein complexes such as the RNA polymerase complexes or the processosome. However, the vast number of interacting proteins (an average protein interacts with several different partners) and the complexity of protein interactions (for example, many proteins are members of distinct protein complexes) (1-3) require efficient means to display and visualize protein interactions. The main approach used toward this goal is the construction of protein interaction networks. Such networks might either describe local subsets of protein interactions such as the relationship of proteins within a protein complex or under certain biological conditions or eventually depict all global protein interactions on the scale of a whole organism. In this minireview, we will survey the major experimental methods applied for the systematic analysis of protein interactions and examine the alternative approaches to deduce protein interaction networks from the different medium-and large-scale data sets.
doi:10.1074/jbc.r110.174052 pmid:21566121 pmcid:PMC3129144 fatcat:k244duhdzbcwjcgzschwl3diyq