Comments on: Domain annotation in trimeric autotransporter adhesins http://freelancingscience.com/2008/04/10/domain-annotation-in-trimeric-autotransporter-adhesins/ visualization, protein science, open science and freelancing science Sun, 11 Dec 2011 09:03:33 +0000 hourly 1 http://wordpress.com/ By: BadA head structure « Freelancing science http://freelancingscience.com/2008/04/10/domain-annotation-in-trimeric-autotransporter-adhesins/#comment-457 Sat, 09 Aug 2008 15:45:19 +0000 http://freesci.wordpress.com/?p=107#comment-457 [...] Domain annotation in trimeric autotransporter adhesins [...]

]]> By: ludo http://freelancingscience.com/2008/04/10/domain-annotation-in-trimeric-autotransporter-adhesins/#comment-379 Sat, 12 Apr 2008 07:03:48 +0000 http://freesci.wordpress.com/?p=107#comment-379 Yes your right its seems that docking will bring no furhter information, but perhaps you can get information normal mode analysis (elesticity and deformation of the trimer fiber). Anyway, if you need to get a trimer, or dimer symetrical you should use http://zlab.bu.edu/m-zdock/ (the paper here http://bioinformatics.oxfordjournals.org/cgi/content/full/21/8/1472). I have test all symetrical docking software, it is the simplest and most efficiant one.

Is there a possibility that your protein act like a porine?

]]> By: Pawel Szczesny http://freelancingscience.com/2008/04/10/domain-annotation-in-trimeric-autotransporter-adhesins/#comment-378 Fri, 11 Apr 2008 16:57:06 +0000 http://freesci.wordpress.com/?p=107#comment-378 Thanks Ludovic. There are a few crystal structures for small parts of this family and for the autotransport domain. Exported parts don’t really resemble typical proteins – for example significant portion of the trimeric fiber is heavily interwound so a monomer doesn’t make sense without other two subunits (see for example 1s7m). We have no idea how the autotransport works, but current assumption is that all three chains go through the pore unfolded and assemble outside of the cell.
So docking of individual monomers is not really necessary, as modelling (when possible) already includes all three subunits (otherwise structure of the monomer collapses in minimization). Thanks for the software suggestion, but I cannot find MZ-Dock anywhere – can you post a link?

]]> By: ludo http://freelancingscience.com/2008/04/10/domain-annotation-in-trimeric-autotransporter-adhesins/#comment-377 Thu, 10 Apr 2008 21:05:45 +0000 http://freesci.wordpress.com/?p=107#comment-377 Congratulation pawel, thats a good news, and bioinformatics is a nice journal!
did you have any structural information? xray or modeling? Is it the trimer that bind the membrane and pass through it ?
Maybe you should be interested on some docking technics that can permit to explore symetrical assembly….For my point of view MZ-Dock is the best ones.
Thus if there is no xray of the trimer or the monomer, maybe it will be interesting to modelize it and explore the different possible trimer…

Congratulation again

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