thanks for putting me straight. This is a very interesting area of science
for me but obviously I'm no expert. I hope the students are learning as
much as me! Please see below for my replies to your questions. Perhaps
there is room for two new terms to describe proteins with same fold but
different functions and proteins with the same function but different
folds.
Regards,
Will
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On Fri, 24 May 1996, Sophia Kossida wrote:
> Dear Will,
>
> hello again let's discuss it.
>
> >Dear Sophia,
> >thanks very much for the information.
> >Let me think it through. As gene duplication leads to the evolution of
> >proteins with same fold but with different functions,
>
> Why do you think that this is the case? What makes you believe that they
> should have different functions? I've done some work on Saccharomyces
I thought, perhaps naively, that gene duplications, as they initially lead
to proteins with same fold and function, offer no evolutionary advantage
until one protein mutates enough to perform some different function
from that of the original protein. On a little reflection, I realise that
a new protein that does the same thing as an old protein but in a
different context could easily offer an evolutionary advantage.
> cerevisiae, E.coli and Haemophilus inflanzae and there are a lot of
> diplucated genes (especially S.cerevisiae) with the same functions!
>
> this suggests that
> >paralogous proteins are in indeed homologous in structure but with
> >different functions? I presume speciation
>
> Speciation or cladogenesis, which is indeed one of the most important
> evolutionary processes, is the creation of two or more species from a
> parental species. That's how I would determine it myself.
>
> is the accumulation of neutral
> >mutations
>
> Why do you think they have to be neutral? That's a long controversial
> subject in literature...
>
My thinking here was that when two species form from a parental species,
at least initally, the vast majority of proteins in the new species will
through necessity carry on working as they did in the parent species.
> which I suppose could eventually lead to the proteins in
> >different structure but the same function (but it seems unlikely?).
>
> It certainly does. The other way round is ok though. I mean proteins with
> different function but same structure.
>
> So I
> >guess my understanding of what Peer ment was correct for the first term
> >but not quite right for the second?
> >
> >John tells me that there are serine proteases with completely different
> >folds but with very similar active site geometry but that this is
> >considered to have occured due to convergent rather than divergent
> >evolution.
> >
> >Regards,
> >
> >Will
>
> Btw I heard Peer's talk too as I attended the one day meeting: Getting the
> most from your Protein Sequence, taking place in London.
>
> I leave you for the moment.
> Cheers
> Sophia
>
> PS I'm off this coming Monday going to Aspen for a workshop so I might not
> be able to answer you quickly enough but I will.
> >____________________________________________________________
> >
> > Will Pitt Tel: 44-171-5806851
> > Crystallography Department, Fax: 44-171-5806803
> > Birkbeck College, w.pitt@mail.cryst.bbk.ac.uk
> > Malet Street, http://www.cryst.bbk.ac.uk/~ubcg08l/
> > London
> > WC1E 7HX
> > U.K.
> >
> >
> >On Fri, 24 May 1996, Sophia Kossida wrote:
> >
> >> Dear Will,
> >>
> >> Two genes are said to be paralogous if they are derived from a duplication
> >> event, but orthologous if they are derived from a speciation event. This is
> >> how the above terms are used, at least, in an evolutionary context.
> >>
> >> Cheers
> >> Sophia
> >>
> >> =====================================================
> >> Sophia Kossida
> >> Merton College
> >> Oxford OX1 4JD
> >> England
> >> e-mail: sophia.kossida@merton.oxford.ac.uk
> >> tel : (44) (0) 1865 271263
> >> fax : (44) (0) 1865 310447
> >> URL : http://users.ox.ac.uk/~mert0223
> >> =====================================================
> >>
> >>
> >>
>
>
>