As Ditlev points out, measuring the channels ignores the flexibility /
dynamic nature of proteins in crystals. Also, if you have any disordered
tag residues or loops, they also occupy space in the solvent channels. That
said, I have found the Doug Juers' lab's program map_channels very useful
for characterizing the dimensions of the solvent channels in a crystal. See
http://people.whitman.edu/~juersdh/Channel_Mapping.shtml
D. H. Juers and J. Ruffin. MAP_CHANNELS: a computation tool to aid in
the visualization and characterization of solvent channels in
macromolecular crystals. J. Appl. Crystallogr. (2014). 47, 2105-2108.
https://dx.doi.org/10.1107/S160057671402281X
https://www.researchgate.net/publication/269041287_MAP-CHANNELS_A_computation_tool_to_aid_in_the_visualization_and_characterization_of_solvent_channels_in_macromolecular_crystals
Regards,
Mitch
Quoting Ditlev Egeskov Brodersen <[log in to unmask]>:
> I guess you could expand your structure using SYMEXP and measure
> across the solvent channels in PyMOL using the Measure tool?
>
> Nevertheless, I don't think this sort of exercise is very useful.
> Crystal soaking is a highly empirical procedure, which in most cases
> is based on pure trial-and-error. Let's say you find that the
> channels are 2 Å too small for your molecule to pass. Would you then
> not do the soak experiment?
>
> I think protein crystals are much more dynamic and flexible than we
> tend to think. Many crystallographers have experienced crystals
> cracking during a soak experiment and still have been able to
> collect useful data. I guess this means that the molecules can flex
> quite a bit and still regain crystal contacts...
>
> We once managed to soak an entire protein (IF1) into crystals of the
> small ribosomal subunit. Amazingly, it worked. If we had thought too
> much about this experiment beforehand, we probably wouldn't have
> done it...
>
> So, my advice: Stop thinking and just do the experiment.
>
> Ditlev
>
> ---
>
> Ditlev E. Brodersen
> Lektor, Associate Professor
> Department of Molecular Biology and Genetics, Aarhus University
> Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
>
> Phone: +45 21669001
> Lab home page: www.bioxray.au.dk/~deb<http://www.bioxray.au.dk/~deb>
> Educational IT portal: curriculearn.dk
>
> On 30 Sep 2018, at 20.58, Murpholino Peligro
> <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Dear all.
> I wonder If any of you know how to calculate the radius along a
> distance for a bulk solvent channel in a protein crystal.
> I can see there is a plethora of programs* to find channels, pores,
> clefts and all the related holes within a protein, but how can I
> take a look at this for the solvent?
> Any tips or suggestions are welcome.
>
> Ps Let's say I want to know if molecule A can diffuse into the
> protein crystal.
>
>
> Thanks
>
> *caver, hole, mole, molaxis, porewalker, hollow just no name a few
>
>
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