Hello We have had an interesting example where the crystal packing seems to have won against the "biological interaction". This is about a "sliding clamp" made of a very symmetric homodimer having the shape of a ring (encircling DNA during its replication). This "beta-ring" had been crystallized alone by the Kuriyan group in P1 (thus there was NCS). In our case, we crystallized it with an additional peptide mimicking the C-term of a polymerase binding to the beta-ring [Burnouf et al, JMB 335(2004) 1187]. We expected a symmetric binding of two peptides/ring (one peptide for each protein in the dimer). However, we observed only one peptide/ring. It turns out that we had obtained exactly the same packing in P1 and that one of the two possible binding sites was engaged in crystal contacts. We estimated the Kd of peptide-ring interaction as being in the µmolar range and that there was only a few percent of beta-rings in crystallization drops being singly occupied. Yet the crystallization process selected this minor species to build crystals with (supposedly) a good crystal packing, rather than "finding" another crystal packing accomodating the doubly-occupied species present in large excess. Our conclusion was that a very modest gain of ca. 2 kcal/mol in the free energy of interaction of singly-occupied beta-rings was sufficient to account for their selection to build crystals against a great majority of doubly-occupied "contaminants". This is exactly the order of magnitude mentioned by Ed Pozharski: a single additional H-bond is enough to account for 2 kcal/mol ! And apparently this may be enough to win against "biological interactions". Let us not forget that there are many processes comparable to crystallization in living cell...
I hope this story makes sense in the frame of this discussion. Philippe Dumas IBMC-CNRS, UPR9002 15, rue René Descartes 67084 Strasbourg cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -----Message d'origine----- De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] la part de Ed Pozharski Envoyé : Monday, June 30, 2008 4:50 PM À : [email protected] Objet : Re: [ccp4bb] Weakest protein-protein complex crystallised The word "weak" is, of course, relative. Free energy of crystallization is roughly 1-2 kcal/mole of crystal contacts (I think I carried this number from Sir Blundell's book, but quick look at papers by Peter Vekilov's group seems to confirm it - am I wrong on this?). I think that crystal contacts are still much weaker than any interaction of biological importance (perhaps I am wrong on this one too and there are important biological protein-protein interaction with 10mM affinity, but I doubt that they are many). On Mon, 2008-06-30 at 10:09 -0400, Patrick Loll wrote: > I hope this isn't too much of a foray into philosophy and semantics, > but can't you argue that the crystals themselves are weak complexes? > And since the energies of crystal contacts are typically very weak, I > would further argue that you should be able to crystallize ANY complex > with an association constant corresponding to energies as low as those > associated with crystal contacts. Of course, it's not guaranteed, any > more than getting a crystal is guaranteed--you need some luck. > > > Of course, it's Monday AM, and I haven't approached my asymptote for > caffeination. Am I talking through my hat? > > > Pat > > > > > On 29 Jun 2008, at 3:36 PM, Derek Logan wrote: > > Hi, > > > > > > Can anyone advise me what is currently the weakest protein-protein > > complex yet crystallised? Google searching turned up a paper from > > the Tromsø crystallography group (Helland et al. 1999, JMB 287, 923– > > 942) in which a complex between beta-trypsin and a P1 mutant of BPTI > > with a Kd of 68 uM was described as belonging to the weakest > > complexes solved to date, but this article was from 1999 and much > > water has passed under the bridge since then. > > > > > > Thanks > > Derek > > _________________________________________________________________ > > Derek Logan tel: +46 46 222 1443 > > Associate professor fax: +46 46 222 4692 > > Molecular Biophysics mob: +46 76 8585 707 > > > > Centre for Molecular Protein Science > > Lund University, Box 124, 221 00 Lund, Sweden > > > > > > > > > > > > > > > > > > > > > > > > --------------------------------------------------------------------------------------- > > Patrick J. Loll, Ph. D. > > Professor of Biochemistry & Molecular Biology > > Director, Biochemistry Graduate Program > > Drexel University College of Medicine > > Room 10-102 New College Building > > 245 N. 15th St., Mailstop 497 > > Philadelphia, PA 19102-1192 USA > > > (215) 762-7706 > > [EMAIL PROTECTED] > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
