Jim wrote:
> So the final 3D configuration of a protein, and its resulting
> function, are quite robust against noise in the 1D sequence?
It varies a lot with the amino-acid. I think proline and
cysteine would be good examples of amino acids that you
can't substitute without breaking things (proline is I
think essential at certain 2D folds in the protein chain
and cysteine is essential for forming di-sulfide bonds that
hold the final 3D structure more rigidly). However many of
the hydrophobic or hydrophilic amino acids (which probably
serve to drive local-folding rates) can probably be substituted
without having too much of an effect on the end result.
There are always a few amino acids in the enzyme catalytic
sites or determining the size of an ion pore for example,
that you absolutely cannot substitute without significantly
damaging or even breaking the function.
I don't know whether or not we know how sensitive changes
would be from a global perspective. Eugene might have a better
idea than I. One thing that I do know is that most of
the current structures are probably sub-optimal. We can
improve things a lot with some "conscious" engineering.
Robert
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