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] http://crg.ubc.ca/VanPetegem/
