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Energetics of the unfolded state

Louis Hom lhom at OCF.Berkeley.EDU
Tue Jan 18 21:09:04 EST 2000


So, I've been thinking a little bit about changes to the unfolded state
that might help favor the folded state, and I've got this question that I
hope I can phrase clearly.

Let's say you have a polypeptide that adopts a certain fold.  And let's
make the wild assumption that the order of the amino acids doesn't matter
(i.e., only the composition of the chain is important, not the positions).

The limiting cases, then, would be 1) the amino acids (hydrophobic, polar,
charged) are distributed evenly/randomly along the chain; and 2) all of
the hydrophobics are grouped together, all the polar residues are grouped
together, all of the charged are grouped together.

My question is:  would you expect any interesting difference to exist
between unfolded case 1 vs. unfoled case 2?

It seems like people normally assume that unfolded chains of the same
composition will behave identically, but it seems like the water would
notice if, for example, all of the hydrophobic residues were grouped
together at one end of the molecule.
-- 
______________________________________________________________________________
Lou Hom >K'93			     
lhom at ocf.berkeley.edu		
http://www.ocf.berkeley.edu/~lhom/ 	    




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