Protein similarity via hydropathy plots?

[Shaun D. Black]

Michael Coyne asked how to discern if two proteins are related by looking 
at their hydropathy plots.  Yes, they looks like a bunch of wiggles, but 
there's gold in them thar hills.  In fact, Sweet and Eisenberg (J. Mol.
Biol. 171: 479-488 (1983)) showed that correlation of sequence 
hydrophobicity measures similarity in the 3D structures of proteins.
So, even though we have no robust way to interpret the 'wiggles', if two 
proteins share similar patterns, it makes a powerful statement about the 
folding potential being similar.

The actual comparison can be done a bunch of ways.  Most folks simply plot 
the two profiles one-on-another and visually examine the similarity or 
difference between the two.  This usually suffices because different 
sequences, unless related, really do have different hydrophobicity profiles.
If you want to get quantitative, an RMS deviance calculation is in order.  
Subtract hydrophobicity values of both sequences complementary residue by 
residue, square each result, take the square root, and finally sum all 
theses and divide by the number of residues compared.  An RMS deviance of 0 
indicates identity, and the further you get from zero, the greater the 
deviance will be (up to 'infinity').  A problem that arises with this 
approach is that homologous structures usually _don't_ align perfectly due 
to differences in loop sizes.  So, the RMS value of the one part of the 
sequence may be low, but increases greatly beyond the loop due to a 'frame 
shift error'.

That's all for now.  Hope this helps.  Cheers,  Shaun
  =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 
  = Shaun D. Black, PhD   | Internet:     shaun at jason.uthct.edu         = 
  = Dept. of Biochemistry | University of Texas Health Center, at Tyler = 
  =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=