protein design using computational methods

Paul Barton-Davis pauld at
Thu May 16 19:59:53 EST 1991

In article <2158 at> toms at (Tom Schneider) writes:

>No, there have been several attempts reported in the literature, even a case of
>a the construction of a catalytic protein.  Sorry, I don't have that reference,
>but I think there was a paper in nature within the last year.  Dickerson, I
>believe, has been working on constructing bundles of alpha helices and beta
>sheets.  Also, the the emerging field of nanotechnology, it is recognized that
>it well may be easier to design proteins from scratch than to figure out how
>they evolved in nature.  Look at the sci.nanotech news group for discussions.

On the other hand, there are a number of well known cases (I've been
out of research in this area for 4 years, so your guess at names is as
good as mine) of:

	1) proteins of very similar sequence folding into
		rather different conformations, even at the secondary
		level (helices and sheets)

	2) proteins of quite different sequence folding into
		rather similar conformations.	

So, with a perspective that's a little stale, I would have said that
Tom's description doesn't do the problem justice: we don't understand
how proteins fold, whether they are synthetic (ala Drexler) or native.
Although there are a few successful examples of predicting what will
happen to a given protein when it is allowed to fold up, they so far
seem not to have elucidated any fundamental understanding of the
process. Until that happens, it may well be that any further successes
will continue to represent good luck rather than any engineering
capability as wanted by the nanotech folk.

Perhaps someone with a newer perspective on the problem of protein
folding could comment on this, if any such person actually *reads*
this group ! I worked at EMBL in the biocomputing group there for a
year, but got too hooked on computers and came to the conclusion that
the protein folding problem is at least a decade away from being solved.
Paul Barton-Davis <pauld at> UW Computer Science Lab	 

"People cannot cooperate towards common goals if they are forced to
 compete with each other in order to guarantee their own survival."

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