[RASMB] A Complicated Equilibrium Problem

[James Cole]

Hi Eric:
Regardless of whatever software you use, It seems unlikely that you  
would be able to reliably fit data to such a complicated model and I  
agree with John Philo that it would be much better  to clean up the  
sample before you do the SV. Do you know if all species you mentioned  
are participating  in a  reversible equilibrium?  If you have some  
irreversible forms, either monomer or oligomer, you might be able to  
remove them by gel filtration. It can be useful to take the monomer  
and oligomer fractions off the column and either rerun them on the  
column or do SV experiments to determine whether the system is  
completely reversible.   Alternatively, can you rule out that you  
have  an indefinite association where the system polymerizes  to form  
dimer, trimer, tetramer, etc. and goes on beyond hexamer at higher  
concentrations?

Jim Cole

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On Jan 14, 2008, at 2:04 PM, Eric Salgado 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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