<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=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
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.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:433134592;
mso-list-type:hybrid;
mso-list-template-ids:470967128 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l0:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l0:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l0:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1
{mso-list-id:514806704;
mso-list-type:hybrid;
mso-list-template-ids:-1517670420 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l1:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l1:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l1:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l2
{mso-list-id:572396984;
mso-list-type:hybrid;
mso-list-template-ids:-290183426 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l2:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l2:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l2:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l2:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l3
{mso-list-id:675306457;
mso-list-type:hybrid;
mso-list-template-ids:34630106 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
@list l3:level1
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level2
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level3
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l3:level4
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level5
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level6
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
@list l3:level7
{mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level8
{mso-level-number-format:alpha-lower;
mso-level-tab-stop:none;
mso-level-number-position:left;
text-indent:-.25in;}
@list l3:level9
{mso-level-number-format:roman-lower;
mso-level-tab-stop:none;
mso-level-number-position:right;
text-indent:-9.0pt;}
ol
{margin-bottom:0in;}
ul
{margin-bottom:0in;}
--></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-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Hi Prasun-<o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1">How different is the atomic composition of your non-natural amino acids from the natural ones?
<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1">Is there any charge present on the aa structure?<o:p></o:p></li></ol>
<p class="MsoNormal">If the answers are:<o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l3 level1 lfo2">Not much different<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l3 level1 lfo2">No<o:p></o:p></li></ol>
<p class="MsoNormal">then you can substitute the vbar of the aa with the nearest matching aa.
<o:p></o:p></p>
<p class="MsoNormal">If the answers are:<o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo3">A lot<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l1 level1 lfo3">No<o:p></o:p></li></ol>
<p class="MsoNormal">then you can use the rules determining the vbar from atomic composition and bonding (single versus double). This should get you to ~1% accuracy. There is a table in Cohn and Edsall that can help, and I am pretty sure that there is a similar
(perhaps broader) table in the wonderful “Thermodynamic Data for…” book.<o:p></o:p></p>
<p class="MsoNormal">If the answers are:<o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l2 level1 lfo4">either not much different or a lot<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0in;mso-list:l2 level1 lfo4">Yes<o:p></o:p></li></ol>
<p class="MsoNormal">This is where a less accurate result probably will be obtained. You can get a good estimate of vbar from the atomic composition for the uncharged version of the aa. The presence of the charge will decrease the vbar. You might get an idea
as to how much it is decreased from the literature. I believe Steve Perkins paper on vbars addresses this. In general, the reduction in vbar due to charge is between 0.05 and 0.08, but there will be uncertainty in how much reduction because of variation due
to the aa context. What I have done in the past is simply increase the uncertainty in my measured parameters by varying vbar over a reasonable range.<o:p></o:p></p>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
<p class="MsoNormal">Tom<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b>From:</b> RASMB [mailto:rasmb-bounces@list.rasmb.org] <b>
On Behalf Of </b>prasun kumar<br>
<b>Sent:</b> Friday, September 29, 2017 3:46 AM<br>
<b>To:</b> Rocco Mattia <mattia.rocco@hsanmartino.it><br>
<b>Cc:</b> rasmb@list.rasmb.org<br>
<b>Subject:</b> Re: [RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Hi Mattia and the group:<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank You for the response. I installed US-SOMO and just to check whether it is working for peptides with non-natural amino acids, I used one PDB ID (1GOE). It contains DPN and AIB. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Program says it has got unrecognised residues and asked me to take the average value or stop processing......<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I chose the first option and got the V-bar value. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Now the question is whether considering the average values for the non-natural amino acids is a good idea or not.... If no then do you think I should also go back and refer to the "bible". <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I am doing my experiments in PBS+Water solvent (pH 7.4)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Regards<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Prasun <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal">PRASUN (ASHOKA)<br>
Desire + stability = Resolution<br>
Resolution + Hard work = Success<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Thu, Sep 28, 2017 at 10:49 AM, Rocco Mattia <<a href="mailto:mattia.rocco@hsanmartino.it" target="_blank">mattia.rocco@hsanmartino.it</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class="MsoNormal">Hello Prasun,<br>
<br>
if you have a PDB file for your peptide, you can try uploading it in US-SOMO and see if the non-standard AA are recognized and a vbar calculated.<br>
<br>
Otherwise, the computations are a bit complicated... we usually do them, when facing non-standard residues, using an Excel worksheet based on the "bible" for vbar calculations: Durchschlag and Zipper, Prog. Colloid Polym. Sci. 94:20-39, 1994<br>
<br>
Hope this helps!<br>
<br>
Mattia<br>
<br>
________________________________<br>
<br>
From: RASMB on behalf of prasun kumar<br>
Sent: Thu 9/28/2017 11:34 AM<br>
To: <a href="mailto:rasmb@list.rasmb.org">rasmb@list.rasmb.org</a><br>
Subject: [RASMB] Regarding V-bar calculation of peptide containing non-natural amino acid<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
<br>
Hi All:<br>
<br>
I have a peptide that contain non-natural amino acids. My query: how to calculate the V-bar of this peptide?<br>
Any suggestions will be really helpful to me.<br>
<br>
Regards<br>
Prasun<br>
<br>
PRASUN (ASHOKA)<br>
Desire + stability = Resolution<br>
Resolution + Hard work = Success<o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>