It seems to me that "concentration" is a statistical, macroscopically-derived concept like temperature or pressure which gets exceedingly weird when applied to microscopic phenomena. One weirdness is, I guess, that the somewhat arbitrary size of the box you mentioned makes a huge difference in the number one calculates for concentration, although it does not change the actual situation at all. Nevertheless, I guess one has sometimes to use the concept to apply macroscopically-derived parameters to structures, such as binding constants. Since the application of the concept of "concentration" to structures involves strange, potentially paradoxical things, then, I was wondering what was the reason for wanting to get into the risky business in the first place?
JPK On Wed, Jun 20, 2012 at 6:08 PM, Filip Van Petegem <[email protected]> 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] > http://crg.ubc.ca/VanPetegem/ -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
