[ssml] Re: Slides to demonstrate conservation of protein structure?

[Brian Foley]

Dear Dan,

    Ben McMahon at Los Alamos National Lab, has done a lot
of work on exactly the thing you are describing, applied to the
tyrosine and serine/threonine kinases:
http://cellsignaling.lanl.gov/structure/kinase/kinase.html
    Many of the kinases have been crystallized and their structures
determined by X-ray crystallography, and although their primary
amino acid sequences are highly variable they all have quite
similar structures.
    Ben's web pages are a bit difficult to navigate, to find all of the
information that you might want.  I find that I just have to "poke around"
to find the 3D Structures such as:
http://cellsignaling.lanl.gov/structure/kinase/ste/A/pak1.html
which shows JPEG images of a sub-family of kinases.  And from
there you can find alignments, X-ray crystal structures, and
PDB file format structures of the other sequences which have
not been actually crystallized but the structures have been built
by "homology modeling" based on the alignment and known structures.
    His site does not contain exactly the slides/images you are looking
for, with one structure super-imposed on another, but I suspect Ben
has done a lot of that, and his site does have a lot of multiple sequence
alignments that are based on structural similarity.  So you could quickly
take those same protein sequences and see if tools such as CLUSTALW
create a similar alignment or not.

Brian T. Foley, PhD
HIV Genetic Sequences, Immunology,
Drug Resistance, Protein 3D Structures, and
Primate Vaccine Trials Databases
http://www.hiv.lanl.gov
btf at lanl.gov
(505) 665-1970

----- Original Message ----- 
From: "Dan Bolser" <dmb at mrc-dunn.cam.ac.uk>
To: "Rasmol Mailing List" <rasmol at lists.umass.edu>
Cc: "Sequence Search Mailing List" <ssml-general at bioinformatics.org>
Sent: Friday, October 08, 2004 4:13 AM
Subject: 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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