> 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:[log in to unmask]] On Behalf Of
> Keller, Jacob
> Sent: Friday, June 27, 2014 3:07 PM
> To: [log in to unmask]
> 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:[log in to unmask]] On Behalf Of
> Bernhard Rupp
> Sent: Friday, June 27, 2014 9:00 AM
> To: [log in to unmask]
> 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:[log in to unmask]] On Behalf Of
> Boaz Shaanan
> Sent: Friday, June 27, 2014 2:26 PM
> To: [log in to unmask]
> 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: [log in to unmask]
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
>
>
>
>
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Reza
> Khayat [[log in to unmask]]
> Sent: Friday, June 27, 2014 2:00 PM
> To: [log in to unmask]
> 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
> =
>
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