Re: "homology / similarity" of proteins

Sophia Kossida (
Fri, 24 May 1996 20:38:05 +0000

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
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

Why do you think they have to be neutral? That's a long controversial
subject in literature...

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

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.

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,
> Malet Street,
> 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:
>> tel : (44) (0) 1865 271263
>> fax : (44) (0) 1865 310447
>> URL :
>> =====================================================