Degradation of nitrile-containing ionic liquids but how?

It is well known that soil bacteria and fungi bioremediate nitrile containing compounds to get at their nitrogen, and that nitrilase/nitrile hydratase pathway enzymes in a range of bacteria/fungi are amenable to such a transformation. A colleague of mine, Steve Cummings, reviewed this area a few years back in a paper entitled "The current and future applications of microorganisms in the bioremediation of cyanide contamination". One possible source of environmental cyanide contamination that Steve didn’t foresee was that from ionic liquids. These have been the subject of a lot of enthusiasm in green chemistry circles as they offer immensely useful solvation properties with no appreciable vapour pressure. Their use on anything other than a laboratory bench scale has met some resistance because of concerns about their environmental toxity. A recent paper entitled “Biodegradation potential of cyano-based ionic liquid anions in a culture of Cupriavidus spp. and their in vitro enzymatic hydrolysisby nitrile hydratase” by Stefan Stolte and co-workers in Environmental Science and Pollution Research has looked at biological hydration/hydrolysis of ionic liquids containing cyano groups.

After trying an organism, they have used a couple of Sigma enzymes to see if these will process their choice of ILs. They discover that the Sigma nitrilase isn’t interested but the Sigma NHase is quite happy to turnover. But I do wish that this information went further. Sigma does not tell you what the source organism(s) for their Nase and NHase enzymes is/are, merely that they are recombinant from E. coli. There is so much variation in substrate selectivity for both classes (for instance, glance at the slice of Steve’s Table 1 below) that getting a positive or a negative hit from a single example of unknown origin tells you not much at all in general.

Sol-gel encapsulation of Cobalt centred nitrile hydratase

The nitrile hydratase from Pseudonocardia thermophila is one of the most stable NHases currently described. It is cobalt centred, and one strain of it has an entry in the PDB. Holz and co-workers have just published a paper entitled "Acrylamide Production using Encapsulated Nitrile Hydratase from Pseudonocardia thermophila in a Sol-gel matrix" in the Journal of Molecular Catalysis A. They show that their system is able to convert acrylonitrile to acrylamide neatly, demonstrating the advantages of their enzyme support system in terms of increasing the robustness of these still rather sensitive enzymes. Interesting to me is that their orthosilicate sol-gels boost this enzyme's stability in methanol to take as much as a70% v/v mix happily.

Nitrile hydratase in March's Advanced Organic Chemistry

As a graduate student, March's Advanced Organic Chemistry was my "go-to" text for leading references for synthetic chemistry questions. It was an incredibly thick book with an extraordinary number of references, and it has only increased in size since my days in TCD, and it is now in its seventh edition.
As my indexing system these days needs more key strokes to navigate than is needed to find things on the Web using Google, I decided to find my first paper on nitrile hydratase online to see which substrates I should have in my "interesting nitriles" cupboard which were ortho-substituted. Sure enough the paper was there but so also was a link to that paper as a reference in March. Yes, it's reference 103 on page 1080 of the seventh edition, as a reference to consult about amide formation though the reason for its inclusion is a bit weird. Anyway, I am very pleased!

Making an approximate 3D model of an enzyme

Sometimes we want to check out how an amino acid sequence from a database might translate into a 3D dimensional structure. This is straightforward enough if there exists an x-ray crystal structure for that exact enzyme in the Protein Data Bank or, like often happens in the nitrile hydratase class, there is very limited variation within sequences so overlaying a short portion of the sequence "by eye" on an existing enzyme is possible.
We are currently working on nitrilases, and despite increasing interest in their use as biocatalysts, the number of nitrilases (i.e. enzymes that convert nitriles to carboxylic acids not the other looser biochemical definition) which exist as structures in the PDB s precisely one. It is from Pyrococcus abyssi and is pretty much restricted in substrate tolerance to small aliphatic nitriles like fumaronitrile. It should not be a surprise that it isnt a great model for many other nitrilases.
If the PDB has come up short we tend to use a link out of the Uniprot database to give a prediction of 3D structure. So if you want to see an estimate of what the nitrilase from Aurantimonas manganoxydans looks like, than the link labelled "ModBase" under the subtitle "3D structure databases" leads you to a page of predictions and further tools. For this specific enzyme it is suggested that a mouse nitrilase superfamily structure contains the best 3D match.