by Peter Nollert
October 3, 2009 08:15
I just saw this new paper published in Acta Cryst F on the topic of heavy atom derivatization:"How to get the magic triangle and the MAD triangle into your protein Crystal" Acta Cryst. (2009). F65, 1068-1070 by T. Beck, C. E. da Cunha and G. M. Sheldrick.
To tell you the truth, had I reviewed the paper, the word 'magic' would not have made it into the paper (see may rant about a similar, delusional topic here). Otherwise, this is a really nice methodological paper, describing a new class of heavy atom compounds and optimized ways to incorporate these into protein crystals by either cocrystallization or soaking. The resulting derivatized protein crystals can be used to "...provide easy access to experimental phasing" via MAD or SAD techniques.
I'm particularly glad that the experimental procedures for co-crystallization and soaking into pre-grown protein crystals are described in such great detail. This facilitates protein crystallization attempts with your own target and the new compounds. The optimized protocols for cocrystallization or soaking using the compounds I3C or B3C look straight forward: add B3C from a stock solution at a concentration 10X that of the protein and set up crystallizations. I was very pleased to see that they employed the Emerald BioSystems Wizard Screen I.
But I cringed when I read that "Limited amounts of B3C may be obtained by contacting TB". Good luck with this in 30 years time. But the other compound, I3C is advertised as "commercially available as a powder from different chemical suppliers". Since I could not find the supplier info in the paper itself, I went back to my preferred chemistry search engine ChemSpider and was quite disappointed that the compound name spelled out (and used in my a copy-and-paste search) in the introduction of the paper (5-amino-2,4,6-triidoisophthalic acid) did not produce a hit (in retrospect I should have seen that there was a typo, it is 'triiodo').
What now? Pull out the ChemSpider drawing tool to create a 2D structural formula et voila: got the compound listed in its full glory as: 5-amino-2,4,6-triiodo-benzene-1,3-dicarboxylic acid. Curiously, the list of synonyms did contain my first search term - without the spelling error - amongst many others. Thankfully, the list of suppliers was also given and amongst them was
Sigma Aldrich - with a direct link to the proper product page in Sigma Aldrich website.
ChemSpider 'in draw a molecule'-mode and the 5-amino-2,4,6-triiodoisophthalic acid molecule with experimental 4sig anomalous electron density (in a Lysozyme molecule).
But I digress.
The breakthrough discovery in utilizing this new class of heavy atom containing compounds is that our toolbox for experimental phasing has been enriched in a substantial way. Not only do these compounds have the capacity for specific binding, they are inexpensive, have comparatively low toxicity and provide a strong anomalous signal enabling SAD phasing with data collected in-house. What else can you ask for?
Now that's what I call a breakthrough. Nothing magic about it.
Herzlichen Dank, Tobias!