| Identifying Protein Interactions |
While it is convenient to think of proteins as discrete and independent molecules, this is actually an oversimplified view. Many proteins require other proteins or cofactors for activity; and proteins involved in signal transduction, protein trafficking, cell cycle, and gene regulation must interact with other proteins in those processes. Many of these interactions require particular domains called interaction domains. Proteins involved in the interactions contain combinations of interaction domains (for interaction with other proteins) and catalytic domains (for function of the protein). The interaction domain can bind the partner protein, even in the absence of the rest of the protein. Interaction domains are often quite versatile, capable of binding a variety of related ligands. In addition, one protein may contain several different interaction domains. The modular nature of these domains allows the protein to interact with multiple target proteins in the cell; thus it provides a mechanism for integration and control of information from protein to protein in a cell. Such protein-protein interactions form the basis for our current understanding of cell signaling pathways and protein networks that regulate all the activities in a cell.
Because protein-protein interactions regulate the activities of cells, identifying them is critical to understanding cellular processes. Mass spectrometry techniques have been developed for large-scale screening to identify interacting proteins. For example, hundreds of known proteins in yeast were engineered to contain a biochemical tag that would allow the tagged protein to be separated from other proteins in a cell extract. This was done gently so that other proteins bound to the tagged protein would still be attached. The tagged protein, along with any associated proteins, was then analyzed by mass spectrometry. The results revealed that about eighty-five percent of these proteins were associated with other proteins. Although most interacted with many other proteins, in some cases two different protein complexes had at least one protein in common. Among the most intriguing questions to come out of this research were what controls which proteins interact and - for those that interact in multiple complexes - how do these proteins know which complex to join?