[ssml] Slides to demonstrate conservation of protein structure?

[Eric Pettersen]

On Oct 8, 2004, at 9:01 AM, ssml-general-request at bioinformatics.org 
wrote:

> Message: 1
> Date: Fri, 8 Oct 2004 11:13:32 +0100 (BST)
> 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>
> Subject: [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.

Chimera (http://www.cgl.ucsf.edu/chimera) will basically do what you 
want to do here.

> 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.

Chimera's Matchmaker tool will do a naive sequence alignment of the two 
structures (using either Needleman-Wunsch or Smith-Waterman) and 
perform the corresponding structural alignment.  With low sequence 
identity, the Needleman-Wunsch alignment will probably be bad.  The 
Smith-Waterman alignment may or may not be.  Also, the sequence 
alignment that guided the structural alignment can be displayed (and 
saved).

> 3) Show a pure (and simple) structural alignment of the two domains.

If you know what parts of each structure should be aligned, you can use 
Chimera's "match" command to do that.  Otherwise you could use MinRMS 
(http://www.cgl.ucsf.edu/Research/minrms/) which may be a bit much, or 
one of the structure alignment servers on the web, such as CE 
(http://cl.sdsc.edu/ce.html).

> 3.1) Show the sequence alignment based on the good structural 
> alignment.

Once the structures are matched in Chimera, you can use the 
Match->Align tool to show/save the corresponding sequence alignment.

Hope this helps.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu