Re: [ccp4bb] estimate of effective concentration
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: filip.vanpete...@gmail.com mailto:filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] estimate of effective concentration
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/
[ccp4bb] estimate of effective concentration
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/
Re: [ccp4bb] estimate of effective concentration
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 filip.vanpete...@gmail.com 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/ -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
