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<p class="MsoNormal"><span 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 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 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 style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#3F31F7">Best to all,<o:p></o:p></span></p>
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<p class="MsoNormal"><span 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 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""> Rufer, Arne [mailto:arne.rufer@roche.com]
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<b>Sent:</b> torsdag, september 28, 2017 17:46<br>
<b>To:</b> HGSR (Holger Martin Strauss)<br>
<b>Cc:</b> 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">Hi Holger,<o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">Arne<o:p></o:p></p>
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<p class="MsoNormal">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></p>
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<p class="MsoNormal"><span 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 style="font-size:10.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span 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 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 style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><span style="font-size:10.0pt;font-family:"Verdana","sans-serif""><o:p></o:p></span></p>
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<![if !supportLists]><span 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 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 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 style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Other examples in the literature for peptides?
<o:p></o:p></span></p>
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</span></span></span><![endif]><span 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 style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Cheers,
</span><span style="font-size:10.0pt;font-family:"Verdana","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#888888"> </span><span 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 style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#888888">Holger</span><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#888888"><o:p></o:p></span></p>
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