Pleas Help Quick

Simon Andrews simon.andrews at
Fri May 5 03:42:12 EST 2000

Toby Skinner wrote:
> Hello, I have a simlpe question and I really nead an answer quick.

Asking nicely is a better way to get a quick answer than demanding one
(people on usenet will often pass over messages which start with a line
like that....)

> Any protein is made up of amino-acids, it is these that define the overall
> structure and therefore function of the protein.  I know that amino-acids
> can be replaced by other amino-acids without effecting the function of the
> protein.

This is true, to a certain extent - in a protein, many single amino acid
substitutions will produce no apparent change in overall function, but
it would be unlikely that a large number of even conservative changes
would have no effect.  In addition, certain amino acids would probably
be absolutely required to maintain functionality.  In haemoglobin, for
instance, I would imagine that the amino acids which interact with the
iron atoms in the molecule would be difficult to mutate without
impairing the function, as would the groups which goverened the
association of the subunits.

> So if I was able to generate a new say, Haemoglobin protein which has a
> significantly different amino-acid content, does anyone know if (in theory)
> it could be created in the lab and experimented apon?  

It depends what you mean by "generate".  If you mean that you are going
to computationally predict a completely new sequence which will adopt
the same structure, and perform the same function as an existing enzyme
then good luck!!  The forces which govern the folding of a linear amino
acid into a 3D structure are not well enough understood to be able to
make definitive predictions about the final strucutre of a given
sequence - let alone start with a structure and predict a sequence which
would form it.

It would be worth your while reading up the literature on prediction of
protein folding before delving into this subject much further. Try
looking at the best structure prediction methods, and their levels of
inaccuracy, and you will appreciate the scale of the problem you are

A overview of the forces which govern protein structure can be found at;

and a sensible review of techniques for structure prediction (and their
inaccuracies) is at;

What can be done, is to generate protein derivatives with varying
numbers of mutations.  This must usually be done in a stepwise mannar,
evaluating the effect of single and double mutations biochemically, and
then combining them.  In our experience (trying to incorporate as many
methionines as possible into a protein) you don't have to make a huge
number of substitutions before things start to go wrong.

> This is a serious
> question and has implications for some software I have written
> (dissertation) for finding amino-acid sequences which fold into the same
> user specified protein.  The idea is that a useful but toxic protein could
> be enginered in the lab to be non-toxic.

This would largely depend on why the protein was toxic in the first
place. If the activity of the protein proved toxic then there's not much
you can do about that.  If you change the activity then you haven't got
the same protein as you started with.  On the other hand, the toxicity
could come from the antigenic properties of the protein - and these
could conceivably be altered without affecting the functionality - but
this is not a trivial task.

I think you should investigate the literature in this area some more,
and prefereably find a molecular biologist / biochemist, with whom you
can sit down and discuss your proposal

I hope this helps



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