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Protein structure from scratch?

Lluis Ribas lluis at aaRS
Fri Aug 5 11:59:53 EST 1994

Tom Branham (tbranham at mm.wellesley.edu) wrote:
: : This may be laughable, but I need to know.  Can one construct a model protein
: : structure from scratch?  If one has a protein of a few hundred amino acids
: Theoretically possible.  If you manage it, let us know, and we'll drive you
: out to pick up your Nobel prize :-)

I disagree. It is theoretically impossible, since we do not have a full 
theory that explains folding. Not to mention the fact that we are talking about
'a few hundred amino acids' !!!.
I agree with the nobel prize bit though, we can go in my car :-).

: : refinement?  I have been trying to do this in Hyperchem, with much frustration
: : since I can't fold the polypeptide about very well once I've made it.  Is there
: : a way, or am I just trying to do something impossible?  All advice greatly
: : appreciated!
: Unless you are wil.ing to spend a few hundred years of your life, I would not 
: spend too much more time trying to just fold it by hand.  Try to start looking
: at structures for related proteins in the protein data bank to get some idea of
: how the relatives are folded.  At least that will give you some kind of a 
: starting point, or a reference frame.  past that you either have to break the
: problem down into small changes from one of those structures, or start collecting
: xray/nmr data  :-)  :-)  :-)

Totally right !. Forget about the 'de novo' stuff, you don't need it anyway. Use
modeling by homology (whith which there are some succesful stories) and a shorter protein 
than 'a few hundred amino acids '.


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