Biotrans 2011

I am off to Biotrans 2011 next week. I am presenting a poster on nitrile hydratases which I will put up here on my return.

More automated modelling

I had a go at trying to get SWISSmodel to produce a structure prediction for the 3D structure of the single subunit NHase of Monosiga brevicollis. It had a fair stab at it, as I would expect since there are existing PDB files of alpha and beta subunits which match the relevant portions of the chain, but still it isnt right. The placement of the metal ion is the immediate indicator for me that it has gone wrong- I would want the active site in the middle not on an exposed edge.



Considering the similarity of the sequence to the alpha subunit to that in the PDB file 1IRE (left below), and the beta subunit in PDB file 1V29 (middle below), I was expecting something a bit like those to thrown together, with some guess at the histidine-heavy chain linking the two ends (poking out to the right on my guesstimate shown below right).



NCBI numbers for September

It has been a while since I had done the usual text search for "nitrile hydratase" under proteins on NCBI's website. Having done the proper filtering job on this numbers in August, I know there is a lot of duplication, error and bizarre search engine behaviour going on but I do think it shows how quickly the number of vaguely applicable sequences is growing. As of today there are 3066 hits for the target phrase (+63 since July), and 1125 RefSeq hits (+20 in the same period).

Disappointingly there was no change in the number of structures listed on the Protein Data Bank.

It should be possible to 3D printing of enzyme models... but how?

It sends me slightly square-eyed staring at my PC trying to get an idea of the steric requirements for molecules to pass down portals into the active sites of nitrile hydratase enzymes. As a big fan of actual physical models of chemical structures, it would be nice to be able to produce something you could hold in your hand which would complement the computer based view. In my situation this should be relatively simple... there are some nice structures available as PDB files, and just across the courtyard from me there is an engineering lab which specializes in rapid prototyping using the more than slightly magical Z-Corp 3D printer. But how on earth do you convert a PDB file format to a PLY or VRML file that the printer reads? Perhaps naively I thought there would be a site somewhere which you can plug in your PDB file and it spits out something the printer will read. Use of Google to research this is like a step back in time leading to an infinite loop of pages from the turn of the millenium where the crucial link is no longer live, or another link to the Milwaukee School of Engineering or the Scripps Institute who will print a structure for a nice price. Oh well.

New patent from Mitsui

A Google alert has led me to a new US patent from Mitsui Chemicals Inc.

The abstract is very abstract: "A nitrile hydratase variant comprising substitution of at least one amino acid with another amino acid to improve two or more properties of nitrile hydratase by substitution of one or more and three or less amino acids".

The objective of the work under the patent is to produce a NHase variant with improved stability and high initial reaction rate.

It appears to be about Pseudonocardia thermophila variants, but I havent read all 77 pages of it since it tends to dwell on the very many changes to the sequence that they are protecting, both at the amino acid and nucleotide level.