Protein-Protein Interaction

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Proteins are responsible for several functions in a cell ranging from a catalyzing reaction to several complex functions. Protein- protein interaction plays an important role within the cellular machinery for specific functions like signal transduction, translation, transcription, replication, control on Cell Cycle etc. The interaction between protein molecules leads to the formation of a larger protein complexes performing a specific function. Interaction among proteins depend upon various factors associated with the protein itself, such as its amino acid sequence, associated co-factors, and finally most important is the three-dimensional shape of protein. The different forces which help in the protein- protein interaction include various non-covalent interaction such as Van-der Waals force, hydrogen bonds formation etc.

Methods to Detect Protein-Protein Interaction

1).  Two Hybrid System

Two hybrid system is one of the most important method for protein-protein interaction studies. This method is used primarily for initial identification of interacting proteins, not for detailed characterization of the interaction. This method cannot provide thermodynamic and other parameters of protein-protein interaction. There are other methods used for thermodynamic and kinetic studies of the interactions (out of scope of the course) .

The two hybrid system is a genetic method which uses transcriptional factor in order to identify Protein Protein Interaction. Transcriptional factor contains DNA binding domain and transcriptional activation domain. The DNA binding domain refers to the promoters of specific gene and the trancriptional  activation domain helps RNA polymerase enzyme to initiate the transcriptional activity of the gene, thus with the help of these two domains the expression of the gene takes place. The yeast two-hybrid system uses this unique feature of eukaryotic transcription factors. As explained earlier, these proteins consist of a DNA binding domain (DBD) which recognizes and binds to a defined promoter sequence upstream of a gene and an activation domain (AD) which interacts with the RNA polymerase II complex. When the DBD and the AD are expressed as separate polypeptides, transcription will not take place. However, DBD still binds to promoter sequence but is unable to activate transcription. The AD can still interact with the RNA polymerase II complex, but since it is not located near the gene anymore, no transcriptional activation is taking place. The two hybrid systems for study of protein-protein interaction is based on the molecular setup of transcription factor.