In line with this, there are a number of pictures in the literature of the mitochondrial electron transport chain, with the complexes lined up in a row embedded in a membrane, and with yeast complex III still having the Fv fragments it was crystallized with, attached. Only obvious if you are familiar with the shape of the native structure, I guess. Could have been avoided if the crystallographer had removed the Fv fragments before depositing, but that would have been bad for the R-factors.
On 05/09/2017 12:49 PM, Ian Tickle wrote:
Hi Tristan I'm not so sure. The co-ordinates are the result of the experiment. How other people choose to interpret those results is their affair. Taking it to its logical conclusion suppose that we 'damage' the protein by mutating/deleting some residues or adding tags purely for the purpose of getting it to crystallise, do we report the structure of the protein as it is in the crystal, or do we report what it would have been if we hadn't messed with it ? The choice is clear in that situation. Cheers -- Ian On 9 May 2017 at 16:45, Tristan Croll <ti...@cam.ac.uk <mailto:ti...@cam.ac.uk>> wrote: Hmm... this is a bit of a philosophical pickle in my mind. Do we want to model the structure as what it looks like after radiation damage has had its way with it, or what it must have looked like *before* the damage? I can see arguments both ways (and can sympathise with the former if you want to make radiation damage a subject of your manuscript), but this is going to lead to headaches for people who want to make use of the resulting coordinates to study the actual biology of your protein. Personally, I'd strongly prefer the latter approach. Tristan On 2017-05-09 16:06, Edward A. Berry wrote: On 05/09/2017 06:18 AM, Ian Tickle wrote: We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So it's indeed very tempting to say that the CO2 is still there, and presumably making the same H bonds that the carboxylate was making to hold it there. It would not be hydrated to carbonic acid, according to https://en.wikipedia.org/wiki/Carbonic_acid <https://en.wikipedia.org/wiki/Carbonic_acid> : "The hydration <https://en.wikipedia.org/wiki/Hydrate <https://en.wikipedia.org/wiki/Hydrate>> equilibrium constant <https://en.wikipedia.org/wiki/Equilibrium_constant <https://en.wikipedia.org/wiki/Equilibrium_constant>> at 25 °C is called K_h , which in the case of carbonic acid is [H_2 CO_3 ]/[CO_2 ] ≈ 1.7×10^−3 in pure water^[5] <https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-HS-5 <https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-HS-5>> and ≈ 1.2×10^−3 in seawater <https://en.wikipedia.org/wiki/Seawater <https://en.wikipedia.org/wiki/Seawater>>.^[6] <https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-SB-6 <https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-SB-6>> Hence, the majority of the carbon dioxide is not converted into carbo n ic acid, remaining as CO_2 molecules.". It looks like this ignores subsequent ionization of H2CO3 which would be quite spontaneous at neutral pH. However the Wikipedia article also indicates the equilibrium is quite slow (which makes sense- otherwise why would carbonic anhydrase exist?) and it would be a great deal slower in vitreous ice at 100 K. Anyway, I had reached the same conclusion and have modeled a number of the troublesome glutamates as decarboxylated with CO2 hovering above. There is a problem that the remaining CG tends to push the CO2 a little out of the density in some cases, but not a severe clash and it may work itself out with further refinement or manual assistance. eab
