<div dir="ltr">Hi All:<div><br></div><div>I have tried calculating Vbar of the peptides (poly-tyr, poly alanine) from the same article or even the single residues. I have got similar values by UltraScan.</div><div>Here I must say that I am comparing the calculated value (using the formula given in the paper) and Ultrascan.</div><div><br></div><div>I was not able to get the 0.653 vbar value for L-Alanine at 25 C using the same calculation. </div><div>I am getting 0.73849 and Ultrascan gives 0.7400</div><div><br></div><div>Hope I am on right direction.</div><div><br></div><div>Regards</div><div>Prasun</div><div> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature">PRASUN (ASHOKA)<br>Desire + stability = Resolution<br>Resolution + Hard work = Success</div></div>
<br><div class="gmail_quote">On Wed, May 9, 2018 at 3:53 PM, Rocco Mattia <span dir="ltr"><<a href="mailto:mattia.rocco@hsanmartino.it" target="_blank">mattia.rocco@hsanmartino.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p style="margin-top:0px;margin-bottom:0px">Hi!</p>
<p style="margin-top:0px;margin-bottom:0px">Tom, the Durchschlag and Zipper paper indeed describes their advancements over the old Traube method you mention, including how to properly deal with charged groups. So, if Prasum is using their scheme, he should
be fine. To make sure he is implementing it correctly (it's tricky... ;-) ), I suggest that he should first see if he can correctly recalculate the vbar of some amino acids.</p>
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<p style="margin-top:0px;margin-bottom:0px">Cheers - Mattia<br>
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<div id="m_-5228339836095924195divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Da:</b> RASMB <<a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank">rasmb-bounces@list.rasmb.org</a>> per conto di Laue, Thomas <<a href="mailto:Tom.Laue@unh.edu" target="_blank">Tom.Laue@unh.edu</a>><br>
<b>Inviato:</b> mercoledì 9 maggio 2018 16:46:55<br>
<b>A:</b> prasun kumar; <a href="mailto:rasmb@list.rasmb.org" target="_blank">rasmb@list.rasmb.org</a><br>
<b>Oggetto:</b> Re: [RASMB] Vbar for a peptide</font>
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<p class="m_-5228339836095924195x_MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Hi Prasun-</span></p>
<p class="m_-5228339836095924195x_MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">The vbar for an uncharged grouping (I’m not sure what AiB is, but assume it is uncharged) may be calculated from the atomic composition and bonds using the method of
Traube (which adds together the atomic volumes, then subtracts a ‘co-volume’ that accounts for the volume reduction due to the bonding). This is similar to what you are describing. There is a description of how to do this calculation in Cohn & Edsall. The
method is inaccurate for charged species in water due to the water collapse around the charged groups, which reduces the vbar. The measured values given by Cohn & Edsall are for blocked amino acids (or their side chains) in water. By using water, they reduced
the error that accompanies H-bond formation with the solvent (a problem that reduces the accuracy of merely inverting the density of a substance to get its vbar).</span></p>
<p class="m_-5228339836095924195x_MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Best wishes,</span></p>
<p class="m_-5228339836095924195x_MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Tom</span></p>
<p class="m_-5228339836095924195x_MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"> </span></p>
<p class="m_-5228339836095924195x_MsoNormal"><b>From:</b> RASMB [mailto:<a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank">rasmb-bounces@list.<wbr>rasmb.org</a>] <b>
On Behalf Of </b>prasun kumar<br>
<b>Sent:</b> Wednesday, May 9, 2018 10:25 AM<br>
<b>To:</b> <a href="mailto:rasmb@list.rasmb.org" target="_blank">rasmb@list.rasmb.org</a><br>
<b>Subject:</b> [RASMB] Vbar for a peptide</p>
<p class="m_-5228339836095924195x_MsoNormal"> </p>
<p class="m_-5228339836095924195x_MsoNormal"><strong><span style="font-family:"Calibri",sans-serif;color:red">Caution - External Email</span></strong>
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<p class="m_-5228339836095924195x_MsoNormal">Hi Group:</p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">I have gone through most of the discussions on Vbar and related stuff here. However, I thought to put my procedure for discussion...</p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">I have a peptide that consist of 2 AiB residues alongwith other natural residues.</p>
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<p class="m_-5228339836095924195x_MsoNormal">Since, the Vbar for AiB is not available, I was considering AiB as Ala and calculating the Vbar of the peptide. However, if Vbar goes down, it overestimates the Mol. Weight of the assembly. I was bit worried about this fact. Then I came
across the paper by Durchschlag and Zipper in Jl of Appl. Cryst. (1997). In this paper authors have tried to calculate the partial specific volumes of small molecules and polymers based on volume increment method. </p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">After going through the above article, I decided to randomize my sequence such that the constituent residues and their numbers remain same. I calculated the Vbar of both sequences and found no difference in Vbar at 20 C. </p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">I also realized that 2 AiB residues can be replaced by one Ala and one Val. for example:</p>
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<p class="m_-5228339836095924195x_MsoNormal">......AiB AiB........ can be ......AV.....</p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">after replacing AiB AiB by AV, I calculated the Vbar of my peptide. </p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">Here, it is important to note that I am not changing the charged or aromatic residues.</p>
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<p class="m_-5228339836095924195x_MsoNormal">Any suggestion on the appropriateness of my procedure is welcome. </p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal">Regards</p>
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<p class="m_-5228339836095924195x_MsoNormal">Prasun</p>
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<p class="m_-5228339836095924195x_MsoNormal"> </p>
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<p class="m_-5228339836095924195x_MsoNormal"><br clear="all">
</p>
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<div>
<p class="m_-5228339836095924195x_MsoNormal">PRASUN (ASHOKA)<br>
Desire + stability = Resolution<br>
Resolution + Hard work = Success</p>
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</div>
</div>
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