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<br>
Hi Christine,<br><br>
I second what Tom and Borries said. Attached you'll find a key paper by
H. Durchschlag and P. Zipper describing how to compute the vbar of
macromolecules. They have a table with the molar volumes of ions
included. If you happen to have a PDB structure for your protein
including the ions, US-SOMO will compute the global psv, but the caveats
pointed out by Tom and Borries will still apply...<br><br>
Salut - Mattia<br><br>
At 02:02 PM 2/27/2014 +0000, Laue, Thomas wrote:<br>
<blockquote type=cite class=cite cite>Content-Language: en-US<br>
Content-Type: multipart/alternative;<br>
<x-tab> </x-tab>boundary="_000_910F1E6B4D39C34FB33F47E069C64D6365CCA349akersadunhedu_"<br><br>
Hi Christine-<br>
In general, their contribution will be roughly proportional to the
inverse of the metal density in the computation of vbar from composition.
The confounding part is that their ionization will cause electrostriction
of water, if they remain charged when bound. If the ions are bound in
such a way to be neutral (i.e. they are chelated by charged residues),
then the approximation using their density will not be as much in error
as it would be if they remain charged.<br>
Best wishes,<br>
Tom<br>
<hr>
<font face="Tahoma" size=2><b>From:</b> rasmb-bounces@list.rasmb.org
[rasmb-bounces@list.rasmb.org] on behalf of EBEL Christine
[christine.ebel@ibs.fr]<br>
<b>Sent:</b> Thursday, February 27, 2014 4:45 AM<br>
<b>To:</b> rasmb@list.rasmb.org<br>
<b>Subject:</b> [RASMB] vbar of protein binding zinc and cupper
ions<br>
</font><br><br>
<h1><font size=2><b>Dear all, </b></font></h1><br><br>
<br>
<h1><font size=2><b>Does somebody know how bound Zn++ or Cu++ ions affect
vbar of proteins?</b></font></h1><br><br>
<br>
<h1><font size=2><b>Thank you in advance </b></font></h1><br><br>
<h1><font size=2><b>Christine</font></b></h1><br><br>
<pre>--
Institut de Biologie Structurale
UMR 5075 CEA - CNRS - Univ. Grenoble Alpes
EPN Campus, 6 rue Jules Horowitz, F-38000 Grenoble
Tel.: +33 (0)4 5742 8570; Fax: +33 (0)4 7650 1890
E mail:
<a href="mailto:Christine.Ebel@ibs.fr">Christine.Ebel@ibs.fr</a>
<a href="http://www.ibs.fr/" eudora="autourl">http://www.ibs.fr</a>
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