[RASMB] another vbar question

John Sumida jpsumida at uw.edu
Thu Sep 28 11:42:44 PDT 2017


Hi Everyone,

Nice discussion on v-bar, thank you for asking the question!

I am wondering about the overall utility of the density contrast approach.
For unknown materials such as CdSe/ZnS qdots or block-polymer micelles which
can be highly heterogeneous and for which a calculation of v-bar may not be
facile, the density contrast approach would seem to have great utility.  In
these cases a densitometric measurement of the density increment can be
severely sample limited.

However, how would the sample heterogeneity in this case affect the v-bar
measurement?  Seems that the best possible outcome here would be some weight
averaged quantity, which, while not precise, may have some utility
nonetheless?

Best regards,
John Sumida
Molecular Analysis Facility
University of Washington

-----Original Message-----
From: RASMB [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Rocco Mattia
Sent: Thursday, September 28, 2017 7:00 AM
To: HGSR (Holger Martin Strauss) <hgsr at novonordisk.com>;
rasmb at list.rasmb.org
Subject: Re: [RASMB] another vbar question

Hello Holger,
 
nice work you're doing with vbar... perhaps it will lead to some correction
factors to be applied to calculated vbars as a function of salt
type/molarity...? ;-)
 
Not surprising that vbar varies with buffer conditions. It's an operational
quantity derived from the molar volume of compounds in solution, and that
volume can change because of ion effects, solvent preferential binding, etc.
The way it's calculated, it's based on measured values for particular groups
under standad conditions (i.e. water at 20 °C, or sometimes at 4 °C).
Clearly, if the molar volumes change as a function of the solution
conditions, so the vbar will change... A notorious case is DNA, for which
measured values of vbar are strongly dependent, say, on Mg content....
 
Although for most standard uses, such as the calculation of MW from AUC or
SAXS, and under "normal" conditions, the errors in vbar won't affect too
much the answer(s) sought (It's a monomer or a dimer....?), if one really
wants to be precise, the vbar should be measured.... apart from the DM500,
differential sedimentation in H2O(16) vs H2O(18) should provide the answer
with much less material (but of course H2O(18) is quite expensive, and
dialysis is required....)
 
Cheers - Mattia

________________________________

From: RASMB on behalf of HGSR (Holger Martin Strauss)
Sent: Thu 9/28/2017 3:48 PM
To: rasmb at list.rasmb.org
Subject: [RASMB] another vbar question


Hello yall,
 
Wow, vbar trending?!
 
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.
 

	
*	How can this be rationalised structurally? 
*	Any tests when droh/dc is more appropriate for Mw /sigma than vbar? 
*	Other examples in the literature for peptides? 
*	Any general comments/anectodes/remarks? 

 
Cheers, 
 
Holger
 
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