<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Verdana;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
h1
{mso-style-priority:9;
mso-style-link:"Heading 1 Char";
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:24.0pt;
font-family:"Times New Roman","serif";
font-weight:bold;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.Heading1Char
{mso-style-name:"Heading 1 Char";
mso-style-priority:9;
mso-style-link:"Heading 1";
font-family:"Cambria","serif";
color:#365F91;
mso-fareast-language:EN-GB;
font-weight:bold;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:"Consolas","serif";
mso-fareast-language:EN-GB;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Verdana","sans-serif";
color:#3F31F7;
font-weight:normal;
font-style:normal;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-GB;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:8.5in 11.0in;
margin:85.05pt 56.7pt 85.05pt 56.7pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7">Bonjour Christine,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7">Just a thought, a little besides the indeed interesting question, what “really” is happening. Not knowing your exact question and the system under study, I
would venture that for most cases it could be sufficient to define your solute as the metal-free entity and the metal as a solvent component. This way, you will still be able to study metal-dependent oligomerisation changes with changes in [metal ion]. For
studying metal ion binding to peptides without changes in the oligomerisation per se, you might still get enough
<i>precision</i> for (1-vbar rho)M from an SE-gradient to back-calculate the change in vbar. Coupled changes in shape/hydra-solvation-whatever you could get by combining this with measurements of the diffusion coefficient, which is independent of the solute
density. Thermodynamic information for the metal binding you could get from other, mass-independent methods.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7">But still, for further reference, it would be nice to have someone bite the bullet ( and working with insulins, I’m not pointing fingers here).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7">Cheers, Holger<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> rasmb-bounces@list.rasmb.org [mailto:rasmb-bounces@list.rasmb.org]
<b>On Behalf Of </b>Mattia Rocco<br>
<b>Sent:</b> Thursday, February 27, 2014 6:46 PM<br>
<b>To:</b> Laue, Thomas; EBEL Christine; rasmb@list.rasmb.org<br>
<b>Subject:</b> Re: [RASMB] vbar of protein binding zinc and copper ions<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><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>
<br>
<o:p></o:p></p>
<p class="MsoNormal">Content-Language: en-US<br>
Content-Type: multipart/alternative;<br>
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<o:p></o:p></p>
<div class="MsoNormal" align="center" style="text-align:center">
<hr size="2" width="100%" align="center">
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a> [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> <a href="mailto:rasmb@list.rasmb.org">rasmb@list.rasmb.org</a><br>
<b>Subject:</b> [RASMB] vbar of protein binding zinc and cupper ions<br>
<br>
</span><o:p></o:p></p>
<h1><span style="font-size:10.0pt">Dear all, </span><o:p></o:p></h1>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
<br>
<o:p></o:p></p>
<h1><span style="font-size:10.0pt">Does somebody know how bound Zn++ or Cu++ ions affect vbar of proteins?</span><o:p></o:p></h1>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
<br>
<o:p></o:p></p>
<h1><span style="font-size:10.0pt">Thank you in advance </span><o:p></o:p></h1>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<h1><span style="font-size:10.0pt">Christine</span><o:p></o:p></h1>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Institut de Biologie Structurale <o:p></o:p></pre>
<pre>UMR 5075 CEA - CNRS - Univ. Grenoble Alpes<o:p></o:p></pre>
<pre>EPN Campus, 6 rue Jules Horowitz, F-38000 Grenoble <o:p></o:p></pre>
<pre>Tel.: +33 (0)4 5742 8570; Fax: +33 (0)4 7650 1890 <o:p></o:p></pre>
<pre>E mail:<o:p></o:p></pre>
<pre><a href="mailto:Christine.Ebel@ibs.fr">Christine.Ebel@ibs.fr</a> <o:p></o:p></pre>
<pre><a href="http://www.ibs.fr/">http://www.ibs.fr</a><o:p></o:p></pre>
<p class="MsoNormal">_______________________________________________<br>
RASMB mailing list<br>
<a href="mailto:RASMB@list.rasmb.org">RASMB@list.rasmb.org</a><br>
<a href="http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org">http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org</a><o:p></o:p></p>
<p><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><br>
</span><span style="font-size:10.0pt;font-family:"Verdana","sans-serif"">ATTENZIONE.<br>
Il presente messaggio ed i suoi allegati devono intendersi ad uso esclusivo dei suoi destinatari e sono confidenziali. Persone diverse dal destinatario, anche ai sensi del D.Lgs. n. 196/2003 , non debbono prendere visione dei contenuti, copiare od inoltrare
l'e-mail a terzi. Se ricevete questo messaggio per errore, Vi preghiamo di cancellarlo, di distruggerne ogni copia e di informarci immediatamente. La mail non è un protocollo sicuro, pertanto IST declina ogni responsabilità in caso di intercettazione o modifiche
del presente messaggio.<br>
<i>WARNING.<br>
This message and any attachments is intended solely for the use of the intended<br>
addressees and is confidential. Any unauthorized review, use, disclosure or distribution<br>
is prohibited. If you receive this message in error, please delete it, destroy all copies<br>
and immediately notify us. Mail is not a secure protocol, therefore IST will not be liable<br>
for interception or amendment of this message.</i></span><o:p></o:p></p>
</div>
</body>
</html>