From: Borries Demeler <demeler@bioc09.v19.uthscsa.edu>
  To  : rasmb@alpha.bbri.org
  Date: Wed, 26 Apr 2000 12:39:29 -0500 (CDT)

Re: variation of local lnks

More to the point:

The protein I am investigating is heme containing, although a small 
population lost the heme group. When I track the association at around
400nm (where heme absorbs) I get a perfect dimer-tetramer-octamer system,
when looking at it at 280, 230 and 207 where also the non-heme containing
subpopulation absorbs, I see this presence of incompetent material.
Clearly, Nonlin is not capable of extracting this information, so I need
to know what models people have used to describe such (apparently frequent)
phenomena. In my case it looks like the heme-containing subpopulation
doesn't produce incompetent species, only the non-heme containing stuff.
This in itself is very interesting biologically in my case.
However I would like to quantify this effect for the monomer-dimer
assoc. constant. However, only at 207 is the conc. low enough for me to 
see monomer, but both populations absorb so I can't separate them. 
The proper model/software should be able to extract the k2 for the 
"competent" species. Has anybody written something like this?

First the question of which assoc. state is incompetent? Does anybody
have experience in telling which one is (OK, I can simulate, but I'd
rather not)? PAGE is not conclusive.  Next, on first glance it seems
that it should be possible to formulate a global model. Any suggestions?

Thanks so much for any pointers, -Borries

> 
> Borries and others; We have frequently run into this situation.  Do you
> notice that there is a trend in the values of lnK, in that they increase
> in a positive direction as loading concentration decreases? If so, that
> is probably due to the presence of incompetent species, not only monomer.
> Irreversible species can be any size--but usually we have found that
> they are at the high end.  Of course it could also be an impurity with a
> MW not related to any of the species that you are trying to fit.
> The best fitting procedure is to solve your
> model so that you are fitting globally all but the last step of the
> association sequence.  Then let that step be fit globally followed by
> letting that step be fit locally.  Then compare rms and systematic errors.
> There are attempts being made to get info re: the species that is incompetent
> and what fractional concentration is present.  Yujia Xu, Dave's last student
> has a dissertation devoted to this which I hope will be published soon.
> You could play around with it in a similar way by simulating various mixtures
> of incompetent species, and seeing what Nonlin will do. Hope this helps.
>                                                         Emory
>