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Archiver > GENEALOGY-DNA > 2010-11 > 1291147444


From: "Brian P. Swann" <>
Subject: Re: [DNA] Predicted structures for mtDNA peptides
Date: Tue, 30 Nov 2010 20:04:04 -0000
References: <0F5E64C46DD44399B2F218BC4B0DD3AA@IanPC>
In-Reply-To: <0F5E64C46DD44399B2F218BC4B0DD3AA@IanPC>


The challenge Ian, as I would see it, is that the mtDNA encodes for only
about half the proteins in the electron transport chain. The other half are
encoded for by nuclear DNA in the conventional manner.

So that about 50 proteins have to assemble into a 3-D array to bridge the
mitochondrial membrane and provide the link from protons to making ATP via
Complexes I to IV of the said chain.

There is a Group at Cambridge that is quite into all that sort of thing
(mitochondrial bioenergetics) - but in my mind there is a very appreciable
translation from the 2-D trans-membrane structures you show to the 3-D
assembly arrangement of each protein in the membrane domain itself.

So I would go and speak with them, or a Group at Newcastle, as you are in
the UK.

Brian

-----Original Message-----
From:
[mailto:] On Behalf Of Ian Logan
Sent: 30 November 2010 14:35
To: Genealogy
Subject: [DNA] Predicted structures for mtDNA peptides

List

Modelling of proteins seems all the rage nowadays ...

So I have had a go at using 'prediction software'
to model the mtDNA peptides; with the expectation that this might give some
idea of the effect of a non-synonymous mutation. See:

http://www.ianlogan.co.uk/TMRjpgs/tmrpage.htm

The models show the peptides all appear to have 'alpha helices' and 'linking
loops'.

And, certainly the effect of some mtDNA mutations can be described very
well.

However there are still many problems and I am not at all sure the
'prediction software' is producing accurate diagrams.

It is possible to convert the simply 2D diagrams to 3D models, which can be
very pretty. But until I have got more correct diagrams - I am not sure this
is really beneficial.

I hope you like the diagrams ..

And, if anyone knows more about this sort of thing I shall be very pleased
to hear from you.

Ian
www.ianlogan.co.uk

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