Dear Filip, I believe that you may find interesting methods, insights and principles to get you going in the following paper:
Wu et al. Transforming binding affinities from three dimensions to two with application to cadherin clustering. Nature. 2011 Jul 27;475(7357):510-3 doi: 10.1038/nature10183 best regards Savvas ---- Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 21 Jun 2012, at 01:08, 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: filip.vanpete...@gmail.com > http://crg.ubc.ca/VanPetegem/
