[ssml] Slides to demonstrate conservation of protein structure?

[Bossers, Alex]

Hi,
Dunno if its too late but here a nice example in prions (mad-cow
disease).
The genes Prn-P (prion protein gene also known as PrP) and the gene
Prn-d (doppel-ganger of PrP or also known as Dpl) have at sequence level
very low homology. However the known structures (determined by whatever
methods) are clearly the same if not almost identical!
A very actual/hot example.

Da stuff (including images):
Science/ PrPs double causes trouble:
http://www.sciencemag.org/cgi/content/full/286/5441/914

At the PNAS paper you can even open images as powerpoint education
slide....
http://www.pnas.org/cgi/content/full/98/5/2352

considering the NMR structures of PrP and Dpl
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-47XNNH2-T
&_coverDate=03%2F07%2F2003&_alid=208550590&_rdoc=1&_fmt=&_orig=search&_q
d=1&_cdi=6899&_sort=d&view=c&_acct=C000026798&_version=1&_urlVersion=0&_
userid=533256&md5=71f9c5ce2bbd8897106e4511f41687af


Regards,
	Alex


> -----Oorspronkelijk bericht-----
> Van: ssml-general-admin at bioinformatics.org [mailto:ssml-general-
> admin at bioinformatics.org] Namens Dan Bolser
> Verzonden: vrijdag 8 oktober 2004 12:14
> Aan: Rasmol Mailing List
> CC: Sequence Search Mailing List
> Onderwerp: [ssml] Slides to demonstrate conservation of protein
structure?
> 
> 
> Hi,
> 
> I would like to demonstrate the well known principal that protein
> structure is more conserved than protein sequence in evolutionary
> time. I am presenting to a group of structural biologists, so I
> want to emphasize the bioinformatic perspective.
> 
> My idea for a series of slides is this
> 
> 1) show two clearly structurally similar (same topology) protein
domains.
> 1.1) show that the two sequences are very different, and result in
>      a 'bad' sequence alignment (somehow visually).
> 
> 2) Show a nieve (and hopefully bad) structural alignment of the two
>    domains based (nievely) on the sequence alignment.
> 
> 3) Show a pure (and simple) structural alignment of the two domains.
> 3.1) Show the sequence alignment based on the good structural
alignment.
> 
> 
> My idea is to convey the importance of structure in recognizing
distant
> homology between domains.
> 
> I want to use a real example using real tools, but I am not sure how /
> which tools to use.Any suggetions? Good demo / bad demo? Naturally I
need
> this done by yesterday, so the simpler the tools the better.
> 
> I will be happy to post the slides somewhere appropriate to share this
> work with the world.
> 
> All the best,
> Dan.
> 
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