Wouldn’t the not-bonded CO2 have a new steric clash with the CG, though? And what happened to the radical that was presumably generated?
Also, I would think solvent-exposed side chains would be more prone to diffusion than buried ones. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Tuesday, May 09, 2017 6:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? Hi Andrew 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 Kh, which in the case of carbonic acid is [H2CO3]/[CO2] ≈ 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 carbonic acid, remaining as CO2 molecules.". Also, diffusion of hydrated HCl in crystalline (hexagonal) ice is apparently negligible at 110 K according to this paper: "Depth-Profiling and Diffusion Measurements in Ice Films Using Infrared Laser Resonant Desorption", F.E. Livingston, J.A. Smith & S.M. George, Anal. Chem., 2000, 72 (22), 5590–9,DOI: 10.1021/ac000724t. Quoting their observations: "at T = 110 K show that the HCl hydrate interlayer is initially well localized at t = 0. The temperature of the H2O/ HCl/ H2O sandwich structure was then raised to T = 190 K for t = 120 s with a constant H2O backing pressure and subsequently cooled rapidly to ∼110 K to terminate further HCl diffusion.”. Now of course measurements of hydrated HCl in crystalline ice may have absolutely no relevance to CO2 in a protein and vitreous ice. It's known that ions diffuse more rapidly in vitreous than crystalline ice because the diffusion mechanism requires 'hopping' between H2O vacancies and there are far fewer of these in crystalline ice. Cheers -- Ian On 4 May 2017 at 11:25, Andrew Leslie <and...@mrc-lmb.cam.ac.uk<mailto:and...@mrc-lmb.cam.ac.uk>> wrote: Dear Ed, I find your electron density quite interesting, because generally (I think, I would be happy to be corrected on this) when de-carboxylation of Asp/Glu occurs due to radiation damage, there is no evidence of what happens to the resulting CO2 group. One interpretation of this is that it diffuses away from the side chain and is effectively totally disordered, so no electron density is seen, but I was surprised that this would always be the case, especially as I would have thought that diffusion would be quite limited at 100K (maybe I’m wrong about that too, but that is supposed to be one reason why radiation damage is less at 100K). If the residual density is due to partial de-carboxylation, then I would have expected density for the CG-CD bond, which is not present (at your chosen contour level). Do many of your Glu side chains have the residual density? Best wishes, Andrew > On 3 May 2017, at 22:19, Edward A. Berry > <ber...@upstate.edu<mailto:ber...@upstate.edu>> wrote: > > > > On 05/03/2017 02:46 PM, Gerard Bricogne wrote: >> Dear Ed, >> >> Have you considered the possibility that it could be a water >> stepping in to fill the void created by partial decarboxylation of the >> glutamate? That could be easily modelled, refined, and tested for its >> ability to flatten the difference map. >> >> Gerard. >> > Actually some of them do appear decarboxylated. Is that something that can > happen? In the crystal, or as radiation damage? > However when there is density for the carboxylate (figure), it appears > continuous and linear, doesn't break up into spheres at H-bonding distance - > almost like the CO2 is still sitting there- but I guess it would get hydrated > to bicarbonate. I could use azide. Or maybe waters with some disorder. > Thanks, > eab > > Figure- 2mFo-DFc at 1.3 sigma, mFo-DFc at 3 sigma, green CO2 is shown for > comparison, not part of the model. > > <decarbox.gif>
