From: Steve Kneizys <spk4@psu.edu>
  To  : rasmb@bbri.harvard.edu
  Date: Tue, 24 Mar 1998 22:30:29 -0500

RE: analysis of heteromeric system

On Tue, 24 Mar 1998 15:33:09 -0800, John Philo wrote:
...
>
>An alternative approach to this multiple minima problem which does NOT 
>require the ability to separate the contributions of different species, and 
>the one that I use in work, is to use numerical constraints to impose mass 
>balance onto the solutions.  It turns out that for each data set only one 
>of the possible solutions is physically realistic, based on the amounts of 
>each protein that were actually put into the cell.  Thus if you can input 
>into the fitter the initial concentration of each species (or at least 
>their molar ratios), and then use this information to penalize solutions 
>which deviate strongly from mass balance, the fitter can avoid the
>physically unrealistic minima and converge on a true and unique solution.
>

This is one of the features I have put into my software.  For each data
file, I require the molar ratios of each monomer to be given.  Then, I have
the fitting function use only one 'total' A0 at R0 as a parameter, use that
value and the ratios to define the other 'total' concentrations of each
monomer, and use the K parameters and mass-balance to solve for the
concentrations of each species at R0 using the Newton-Raphson method.  The
result is that for each iteration of the nonlinear least squares procedure,
the mass balance requirement is satisfied. I chose this method because of
the success using it with NMR and Calorimetric data. 

Steve...
--
Steve Kneizys (spk4@psu.edu)
Graduate Student
Department of Biochemistry and Molecular Biology
Pennsylvania State University College of Medicine
The Milton S. Hershey Medical Center
P.O. Box 850
Hershey, PA 17033