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 '.
LLuis
