There are so many types of protein-protein interactions via various domains, such as SH2 binding (in RTK signaling), Pleckstrin Homology domain (involved in signaling) among others. This site gives a nice list: http://pawsonlab.mshri.on.ca/index.php?option=com_content&task=view&id=30&Itemid=63
Of course, protein-protein interactions rely on the premises of basic biochemistry:
- van-der waals interactions (at the most basic level)
- Electrostatic interactions
- "Lock and Key" model: Some proteins have specific binding pockets for domains of other proteins
- Induced fit
There are many ways to study protein-protein interactions, including, but not limited to
- Pull-down assays
- 2D SDS-PAGE / MS
- Yeast two-hybrid
- Immunoprecipitation
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