Re: Article: On the Origins of Chemical Biodefense


Larry Moran wrote:
> On Sun, 16 Oct 2005 01:41:04 -0400 (EDT),
> Robert Karl Stonjek <rstonjek@xxxxxxxxxxxxxx> wrote:
>
> > On the Origins of Chemical Biodefense
> >
> > The following points are made by R. Liddington and L. Bankston
> > (Nature 2005 437:484):
>
> [snip]
>
> > Random mutations occurring over hundreds of millions of years mean
> > that the component amino-acid sequences of individual domains no
> > longer share any similarity; nevertheless, their evolutionary origin
> > is preserved in their three-dimensional structure.
>
> The other possibiity is that the motifs/domains in different
> proteins do not share a common ancestor. Their structural similarity
> is due to convergence on a common structural motif. In that case,
> the absence of any sequence similarity is evidence that they are not
> evolutionarily related.
>
> There is a controversy in the field of molecular evolution. Some
> people, like me, believe that convergence explains many common
> sequence motifs. We believe it's very unlikely that all traces
> of sequence similarity could be lost in regions that must preserve
> structural integrity while randomly changing all the amino acids
> in order to wipe out sequence similarity. That just doesn't make
> a lot of sense.
>
> Others believe that structural similarity trumps sequence similarity
> when it comes to making decisions about homology. Those people
> believe that all similar structures have evolved from a common
> ancestor. In extreme cases they'll even argue that all zinc
> fingers and all leucine zippers are homologous.
>
Interesting. Could you recommend a review article that discusses
this controversy? Most of the things I have read say that
structure is more strongly conserved than sequence and hence
that structural alignment should guide sequence alignment. I
had never really considered the possibility of structural
convergence.

But ISTM that 'convergence' is not really a good word for the
hypothesis. There is no 'gradualism' in the structural
evolution, is there? The two polymers may evolve to the same
structure, but they don't really 'converge' upon that structure.
You almost have to assume that the final structure arises almost
as a 'saltation'.

Which is not to say that it is impossible for two non-homologous
sequences to have the same structure. When you get right down
to it, there just aren't all that many different structures to
choose from.


.

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