> Here you are starting to mix equilibrium arguments with the previous kinetic arguments.
I don't think I am mixing them; both are relevant. If it cannot diffuse there, forget the kinetics - necessary but not sufficient requirement. Nonetheless, the fact that in high concentrations you can force even weak non-native binders into binding sites (but I reiterate, never in 100% occupancy, at best asymptotically approaching it) is the reason for the many buffer 'ligands' observed in structures (also basis for fragment screening.) > Your movie doesn't include any details of concentration of your dye, nor what its binding constant is to any sites in a protein nor any mention of kon or koff. The movie does not claim to be a study of any specific ligand binding, it simply illustrates soaking. Graphs of concentration vs achievable equilibrium occupancy at different Kds are in separate figures eg 3-40. Cheers, BR Dale Tronrud > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Keller, Jacob > Sent: Friday, June 27, 2014 3:07 PM > To: [email protected] > Subject: Re: [ccp4bb] Solvent channels > > ....And yet halides--even iodide--permeate those same lysozyme > crystals and others entirely in <30--60 sec. > > JPK > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Bernhard Rupp > Sent: Friday, June 27, 2014 9:00 AM > To: [email protected] > Subject: Re: [ccp4bb] Solvent channels > > Just a remark: diffusion is a slow and random-walk process. > Particularly large molecules in viscous media (PEG anybody?) move > (diffuse) slowly in solution. To simply extrapolate from the fact that > the ligand is smaller than the solvent channels to the odds of the > presence of a ligand is a risky proposition. Positive omit difference > density after 'shoot first' as Boaz indicated is a much better indication. And shoot you probably will a lot. > > The little movie below shows how slowly even a small aromatic dye > molecule soaks into a crystal. Total time 10 hrs. > > http://www.ruppweb.org/cryscam/lysozyme_dye_small.wmv > > The literally hundreds of empty ligand structures collected in > Twilight attest to that fact. > > http://journals.iucr.org/d/issues/2013/02/00/issconts.html > > Best, BR > > Science is a way of trying not to fool yourself: The first principle > is that you must not fool yourself - and you are the easiest person to fool. > > R. Feynman, 1974 > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Boaz Shaanan > Sent: Friday, June 27, 2014 2:26 PM > To: [email protected] > Subject: Re: [ccp4bb] Solvent channels > > Hi, > > I'm not aware of a program with an option to display channels in > crystals but if you use any of the currently available molecular > display program and ask to display symmetry-related molecules + > adjacent unit cells, it should give you a good enough idea of the > spaces between molecules. Using programs for calculation of intermolecular distances would also be helpful here. > Independently of the calculation, I would try soaking first and > consult the calculations later (in the spirit of Rossmann's American > method: shoot first ask later). > > Cheers, > > Boaz > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: [email protected] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Reza > Khayat [[email protected]] > Sent: Friday, June 27, 2014 2:00 PM > To: [email protected] > Subject: [ccp4bb] Solvent channels > > Hi, > > I'd like to do some soaking experiments with a relatively large molecule. > Can someone suggest a program/method to display the solvent channels > of a crystal? We have the crystal structure. I'd like to see if the > channels are large enough to allow the molecule to travel to the > hypothesized binding site. > Thanks. > > Best wishes, > Reza > > Reza Khayat, PhD > Assistant Professor > The City College of New York > Department of Chemistry, MR-1135 > 160 Convent Avenue > New York, NY 10031 > Tel. (212) 650-6070 > www.khayatlab.org > = >
