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 <[email protected]>:
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
<[email protected]<mailto:[email protected]>> 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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