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I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?

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Characteristics? They happen between proteins. –  Konrad Rudolph Mar 12 '12 at 23:41
    
characteristics of the interaction type, i.e, what makes a hydrophobic interaction? –  harpalss Mar 13 '12 at 0:20
    
I would suggest asking "what are the various types of protein-protein interactions" –  bobthejoe Mar 13 '12 at 7:33
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up vote 6 down vote accepted

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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jp has a good point - technically there is no 'hydrophobic force' but when computations are done, a hydrophobic term is often made in the calculations. –  shigeta Mar 13 '12 at 4:10
    
Although hydrophobicity isn't a "force", shouldn't it still be included in the answer (creates an entropic advantage)? –  LanceLafontaine Aug 17 '12 at 2:22
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