Protein structure from scratch?

Scott Legrand legrand at tesla.mbi.ucla.edu
Fri Aug 5 17:10:24 EST 1994


In article <170097098S86.FJVAND00 at ukcc.uky.edu>, FJVAND00 at ukcc.uky.edu (Frank van de Loo) writes:
|> Dear Modelers,
|>  
|> This may be laughable, but I need to know.  Can one construct a model protein
|> structure from scratch?  

In principle yes, proteins do it every day.  Unofortunately, we haven't a really
strong clue to the nuts and bolts as to how they do it, just lots of tantalizing
clues and some reasonable constraints.

>If one has a protein of a few hundred amino acids
|> length and various types of data (homology, site-directed mutagenesis,
|> photolabelling, etc), and can come up with a hypothetical super-secondary

If you've got strong homology to a known structure , say >30%, you have a very
good chance of constructing a reasonable model for the protein just by
basing it on this structure.  At that point, modelling tools can then help
you clean it up.

|> or tertiary structure on paper for most or part of it, is it possible to constuct
|> the model in a program that can then display it and be used for further
|> 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

Now if you could do it by hand, you'd make an AWFUL lot of money and you'd
make a lot of scientists (myself included) look pretty dumb :-)...

|> a way, or am I just trying to do something impossible?  All advice greatly
|> appreciated!

It's certainly not impossible, just incredibly unlikely at this stage of
the game...

Scott



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