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 : "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
