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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hi-<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">It is important to realize that vbar is NOT a property of the molecule of interest, so structural information, though useful, is of limited importance.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">The density increment is the proper thermodynamic term for sedimentation. It should be recognized that this term is a system parameter that is focused on what is happening
to the solvent, at low concentrations, and the solution at higher concentrations, as more solute is added. Beyond the effects of electrostriction (which increase the solution density), the density increment can be understood on the combination of excluded
volume and solvent structure perturbation. It seems that the latter is at play with this molecule.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Tom<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> RASMB [mailto:rasmb-bounces@list.rasmb.org]
<b>On Behalf Of </b>HGSR (Holger Martin Strauss)<br>
<b>Sent:</b> Friday, September 29, 2017 4:59 AM<br>
<b>To:</b> Rufer, Arne <arne.rufer@roche.com>; rasmb@list.rasmb.org<br>
<b>Subject:</b> Re: [RASMB] another vbar question<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7">Hej Arne and all,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7">We’re thinking along similar lines here (and thanks for sharing that much here. Question is, where’s the acyl chain for the solvated particle?);
from my experience, the vbar/molar increments for peptides are basically useless, which is why we measure them. Distinguishing a 1-2 equ. Might be doable from sigma alone, but not the difference between a 1-2-3 and 2-4 (e.g). There, you need to fix as many
sigmas as possible, at least in my hands. <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7">Tom, thanks for the density increment comment; that’s of course the bare-bones buoyancy, which is what the particle experiences. Keep it simple.
Still: the vbar, as a composite parameter should be interpretable in “structural” terms (that might be accuracy-limited, I fear). I’ll ask our SAXS people about this. And yes, Heini Eisenberg as well, though insomnia is not my biggest concern right now.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7">Best to all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#3F31F7">Holger<o:p></o:p></span></p>
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<p class="MsoNormal"><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"> Rufer, Arne [<a href="mailto:arne.rufer@roche.com">mailto:arne.rufer@roche.com</a>]
<br>
<b>Sent:</b> torsdag, september 28, 2017 17:46<br>
<b>To:</b> HGSR (Holger Martin Strauss)<br>
<b>Cc:</b> <a href="mailto:rasmb@list.rasmb.org">rasmb@list.rasmb.org</a><br>
<b>Subject:</b> Re: [RASMB] another vbar question<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Hi Holger,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">would preferential hydration play a role at the very high NaCl concentrations you are using? Regarding anecdotes on vbar, I can add that when we worked with acylated peptides the vbar measured by densitometry turned out
to be much smaller than vbar calculated from the aa sequence + modification. We had congruent AUC and SEC-MALLS data showing that certain acylations led to oligomerisation, presumably due to an hydrophobic interaction that became stronger with higher salt
concentration. At that time we argued the effect on vbar could be due to a solvent envelope for packed acyl-moieties that is smaller than that of the separated acyl-moieties. Makes sense? I am curious to read Mattia's comment on this, too.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">Arne<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB">On Thu, Sep 28, 2017 at 3:48 PM, HGSR (Holger Martin Strauss) <<a href="mailto:hgsr@novonordisk.com" target="_blank">hgsr@novonordisk.com</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Hello yall,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">Wow, vbar trending?!<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif">I actually have a question regarding the salt-dependency of the vbar. We are working with peptides modified with some organic linkers and a diacid (between C4-C50,
to give a range). We measure the droh/dc (DMA5000) at different concentrations and calculate the vbar. Controls OK, concentration accurate and measurements reproducible, buffer dialysed. Salt-concentration is varied (NaCl, 5-1500 mM-ish). Turns out the vbar
is considerably different at high salt. (And so is the self-association, btw.) No detergents or denaturants, just some additional phosphate for buffering, besides the NaCl.<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"><o:p></o:p></span></p>
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<![if !supportLists]><span lang="EN-GB" style="font-size:10.0pt;font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">How can this be rationalised structurally?
<o:p></o:p></span></p>
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</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Any tests when droh/dc is more appropriate for Mw /sigma than vbar?<o:p></o:p></span></p>
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</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Other examples in the literature for peptides?
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</span></span></span><![endif]><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Any general comments/anectodes/remarks?<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Cheers,
</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#888888"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#888888"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#888888">Holger</span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#888888"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#888888"> </span><span lang="EN-GB" style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:#888888"><o:p></o:p></span></p>
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