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 : "The hydration <https://en.wikipedia.org/wiki/Hydrate> 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> and ≈ 1.2×10^−3 in seawater <https://en.wikipedia.org/wiki/Seawater>.^[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
