[RASMB] Interpreting SV and SE data

[Peter Schuck]

Hi Eric,

whether or not c(M) is a good way to confirm the molar mass of the trimer 
depends on how much you can shift the population to that state.  If it is 
the predominant species and the peak doesn't shift anymore with higher 
concentrations, then it should work fine according to our experience with 
our systems, and following the theoretical expectations (a reaction 
boundary can be well-described by a single diffusion coefficient - you can 
simulate such data in SEDPHAT [see the workshop handouts for how to do 
that] and re-analyze it with c(s) or c(M) and see at what concentrations 
the approximations break down).  However, without seeing the actual c(s) 
traces for the different concentrations, I cannot say if it is reasonable 
in your case or not.

I agree with John about checking if the s-value makes sense 
hydrodynamically for the trimer.

I don't know how large the aggregates are, but unless they are much larger 
than the highest oligomer of interest, they can cause more trouble in the 
SE analysis than in SV.

Peter



At 01:54 PM 5/29/2008, you wrote:
>Hello all,
>   I have a system for which I've done SV experiments at multiple 
> concentrations that, on increasing the concentration, reveals a peak that 
> starts at an s value of about 2, shifts to a plateau between 2.4 and 2.6, 
> then steadily increases at 2.6. I should point out that all of these 
> peaks are very broad.
>   The c(MW) analysis describes a monomer at low concentrations; dimer at 
> intermediate concentrations; something between dimer and trimer at high 
> concentrations; and finally, as an aggregate starts to form at very high 
> concentrations, a trimer peak is resolved. This trimer peak correlates to 
> our crystal structure, but it appears as if, because of the apparently 
> low association constant and fast kinetics involved with the trimer 
> formation, this fact is masked in the SV data.
>   In order to hopefully rid of this ambiguity, I performed SE experiments 
> in the concentration regime that did not form an aggregate (and therefore 
> apparently only a small amount of trimer), but find that, as far as a 
> species analysis goes, both a model with monomer-dimer or 
> monomer-dimer-trimer present are statistically equal. That being said, 
> the statistics are lower for the later model, while the fit and residuals 
> for both are equally good.
>   With all of this in hand, how can I determine the best SE model to use, 
> and can I say with certainty that the trimer exists in solution from 
> these data?
>
>I know this is a lot, but I would appreciate any help I can get with this 
>problem.
>
>Thank you in advance,
>
>Eric Salgado
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