I would think the first goal is to model the observed data correctly, and then afterwards an accurate "before" model could be inferred.
It seems that it would be extremely helpful to this end to add another column to the .pdb format: a "time constant" for radiation damage for each atom. When set to 0, there would be no decay (default, toggled off in refinement?), and negative and positive values could denote exponential decay (carboxyl) or appearance (CO2). But then, of course, one would also have to set up refinement to use unmerged data. But shouldn't this be done at some point anyway, now that we have the cyber-power to do it? JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tristan Croll Sent: Tuesday, May 09, 2017 11:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? 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
