[RASMB] A Complicated Equilibrium Problem

[John Philo]

Eric,

The program SEDANAL by Walt Stafford includes a model builder so you can do
what you like.

Be aware though that one common complicating factor is that not 100% of your
protein is participating in the mass-action equilibrium. You could have
"incompetent monomer" that does not associate, or irreversible aggregates of
the protein (independent of nickel binding). For example, if you drive
association with nickel, but then chelate away the nickel, do you get back
to 100% monomer?

Overall, my advice would be that often one can make more progress by
cleaning up your samples and getting better data rather than spending lots
of time fitting complex models to bad data.

John

-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of Eric Salgado
Sent: Monday, January 14, 2008 11:04 AM
To: rasmb at server1.bbri.org
Subject: [RASMB] A Complicated Equilibrium Problem


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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