On Mon, 2 Feb 2004, Jim Menegay wrote:
> "Bartosz Milewski" <
[email protected]> wrote in message
> news:<
[email protected]>...
> > Is the similarity between hemoglobin and chlorophyll an accident or did one evolve from the
> > other?
>
> Presumably you mean the similarity between heme and chlorophyl. Hemoglobin is a protein that
> carries heme.
>
> Probably not an accident. There are other related biomolecules, including vitamin B12. It is not
> clear (to me) which was first, if any. However, the words "evolve from" should be used carefully.
> Heme didn't slowly become chlorophyl, if that is the direction that evolution took. Instead, the
> heme production machinery evolved to become chlorophyl production machinery. At least that is a
> better picture than saying that a small molecule evolved, even if the process went through
> several steps.
Interesting distinction dont you think?
Did one metabolic protein slowly become another, or did the specific mechanisms of DNA facilitate
the process of evolution?
Hmmm - hypercycles are too tricky for my brain....
On the topic of the original post.... A structural comparison of protein fold type has proven very
useful in the construction of evolutionary groups of proteins - I am trying to start a project to do
the same for small molecules - Structural Classification of Ligands (SCOL) (re SCOP for proteins).
However - this is not easy - in the given example the similarity between haem and chlorophyl is both
structural and physiochemical - how should we begin to classify chemical structures into an overal
hierarchy?
I beleive such a framework would be a first step towards answering questions like 'which came first'
above. For example - how old is colesterol? - No doubt not as old as Fe4S, but how about glucose?
Anybody want to work on SCOL?
(hopefully)
http://bioinformatics.org/
I know there are many small molecule similarity (searching) algorithms out their - The first step is
to pick a few of these and see what comes out.
Cheers, Dan.