Hi, 'The Role of Diffusion in Enzyme Kinetics' http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367934/pdf/biophysj00672-0040.pdf Mark ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Mark Agacan, Scientific Officer for the Division of Biological Chemistry and Drug Discovery, Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Tel: +44 1382 386095 Fax: +44 1382 345764 Mobile: 07525 451 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
************************************************************ Please consider the environment. Do you really need to print this email? >>> Anastassis Perrakis <a.perra...@nki.nl> 7/5/2010 13:08 >>> Hi Jacob - Sorry if I caused any misunderstanding, but I am not saying that kD is not mattering in cells. Of course it should matter. I am making the distinction that the concentration dependent component of it, k(on), is of less importance, since in the viscous environment of a cell, the chance of two molecules to find each other should be limited by diffusion rates before concentration becomes the limiting factor for their chance to meet and form a complex. The concentration independent component of kD, k(off), the half time that two molecules need to break a complex once formed, I think is what is most relevant in the cell. Although I came across this argument a few times, and I find it convincing, I am not aware of a paper that proves the first derivation, that indeed diffusion rates will be the limiting factor. Unless someone posts the reference, I just got myself an evening project to find it ... A. On Jul 5, 2010, at 0:18, Jacob Keller wrote: 4. The physiological concentration is a bit misleading. First, its clear now that cells have microenvironments, and 'physiological' concentrations are hard to define. Also, in a cell, I think (and I think others tend to agree) that kD plays little role at the end. kD is a combination of k(on) - which is concentration dependent but in a cell very likely diffusion limited - and of k(off) which I think is what matters most in the cell. Can you provide some references about kD not mattering in cells? I had thought it a basic tenet that kD was a major indication of physiological relevence. After all, one could presumably determine a kD for any two proteins, so the order of magnitude of the kD would seem to matter. I hear that your argument is more subtle in considering the elements of kD, but isn't kD usually a rough indicator of k(off), and of course more readily-accessible experimentally? I am intrigued by the idea... Jacob Keller P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 The University of Dundee is a registered Scottish charity, No: SC015096
