[RASMB] A Complicated Equilibrium Problem

[Peter Schuck]

Hi Eric,

if you're able to determine the species concentrations in SV through c(s) 
in SEDFIT or by discrete species analysis in SEDPHAT, it must mean that the 
interconversion is sufficiently slow such that the oligomers to not fall 
apart on the time-scale of sedimentation.  If this is true, then the 
signals from each oligomer still approximately reflect their equilibrium 
populations.  In that case, you can simply use the signals of each of the 
oligomers, convert into concentration, and plug that into any mass action 
law to get the binding constants.

With a system as complicated as yours, even if it is pretty clean, I'm not 
sure if there is a good chance to do much better.  For reasons I've 
outlined previously, I don't think that kinetic rate constants will be 
sufficiently well determined not to have enormous parameter correlations 
and be extremely susceptible from systematic errors arising from slight 
inaccuracies in the assumptions regarding buoyancy and purity.

On the other hand, even if there's slight dissociation during SV, the 
numbers you may be able to get from species analysis may still be pretty 
good ball-park estimates.  You can find out if that approximation works 
well by running your sample at different concentrations. If the s-value of 
the peaks for each species appears independent of loading concentration 
(i.e. only the relative height changes, but not peak position), then this 
should be pretty good.

Peter



At 02:04 PM 1/14/2008, you wrote:
>Hello,
>   I have a system that contains four different molecular weight species 
> of my protein ( monomer, dimer, trimer, hexamer), all mediated by Nickel 
> coordination. I can see this through previous SV experiments, as well as 
> the species analysis model in SEDPHAT. I cannot, however, determine any 
> dissociation constants using any of the pre-existing models in that 
> program. I'm thinking that there might be competing monomer-dimer and 
> monomer-trimer-hexamer equilibriums, or some combination thereof.
>   With all of this in mind, I was wondering if there was a program with a 
> model such as this that I might employ, or if it would be possible to add 
> my own model to such programs as Heteroanaylsis, Sedphat, etc.
>   Thank you for your time and advice in advance,
>
>      Eric Salgado
>      Univ. Cal. San Diego
>      Dept. Chemistry and Biochemistry
>
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