Filip,
if you have a way to measure the fraction bound (say you see two
conformers and your data is good enough to refine occupancies), and if
the binding constant for the two peptides in solution is measurable then
you can derive your "effective concentration". What would that really
tell you I am not sure. For all practical purposes, you have a
monomolecular reaction, because the interacting components are held in
proximity. What is the effective concentration of individual amino
acids in context of protein unfolding?
Cheers,
Ed.
On 06/20/2012 07:08 PM, Filip Van Petegem wrote:
Dear crystallographers,
I have a question concerning effective concentration. Say you have a
crystal structure whereby two loops, each part of a different domain
but within the same molecule happen to be juxtaposed and can form an
interaction. The loops have some degree of flexibility, but are
ordered when interacting. The domains on which they are attached have
a rigid configuration due to the remainder of the structure. The
interaction is potentially very weak and mainly driven by the fact
that the effective concentration is extremely high.
The question: how can one obtain a rough estimate of the effective
concentration of these two juxtaposed loops? The simple
straightforward answer would be to just divide number (1 each) by
volume (some box drawn around the loops), and convert this to molar.
That's easy. However, this is over-simplified and really an
underestimate of 'effective' concentration, because these loops cannot
rotate freely when attached to the domains. Hence, there are
constraints that allow them to interact more readily compared to the
isolated loops within the same box. So I'm looking for a model that
also takes limited conformational freedom into account.
If anybody has any pointers to some reference text or paper that has
performed such an analysis, I would be very interested.
Regards,
Filip
--
Filip Van Petegem, PhD
Associate Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: [email protected] <mailto:[email protected]>
http://crg.ubc.ca/VanPetegem/
