QUESTIONS: alpha-helix "signals" in proteins

Andrew Torda torda at igc.chem.ethz.ch
Fri Jul 15 03:35:40 EST 1994

d43162a at nucc.cc.nagoya-u.ac.jp (Toshiya Endo) wrote
[... lots deleted ...]
>The tendency of proteins to fold fast to native conformations may not be 
>sequence independent.  Nature may well have selected proteins that can 
>fold fast, since polypeptides that remain unfolded in the cells are degraded 
>by specific proteases.  Recent works by Karplus' group (Nature 369, 248-
>251) suggest that such fast-folding sequences may give structures that 
>are thermodynamically stable. 

Perhaps more specifically on the issue of sequence determining
folding, you should look at News and Views in Nature 370, 13.
That will refer you to Shakhnovich (1994) Phys Rev Lett, 72,
3907.  This paper presents more arguments that folding is
definitely not sequence independent.
Their approach is cunning since they first optimise their
sequence before doing a lattice simulation of folding.
This posting is not merely my opinion.
It is the official position of my employer,
the Swiss Federal Institute of Technology.
(Andrew Torda,  Computational Chemistry, ETH, Zurich,  torda at igc.chem.ethz.ch)

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