Wednesday, November 14, 2007

Ring around the protein...

Blogging on Peer-Reviewed Research
One of the journals I monitor by RSS is Nucleic Acids Research, and the usual steady flow of new items has become a torrent, mostly about databases. Yes, the annual Database Issue is on its way and the Advance Access shows the signs. And, it's all Open Access.

Every year this issue grows and grows, and each year I skim through all the little niche databases. They may be small and esoteric, but somebody has a passion for that niche & that's great!

I've always liked oddities & anomalies in biology: the rules are useful, but the mess is fascinating. Somewhere in my undergraduate days I came across the fact that there were known examples of circularly permuted proteins, proteins whose final sequence is attained by moving a segment from the tail end around to the front. But somehow the existence of proteins whose mature form is a circle (via a post-translational step) had escaped me. But now that void is filled, as I can loop around to CyBase, a database of cyclic proteins and peptides.

Why circlets? Well, one obvious advantage is two fewer free ends for proteases to make mischief of -- and many of these proteins are protease inhibitors. Indeed, the stability extends to other abuses, with the suggestion that these might make interesting scaffolds for drug development. Circles also make for attractive sequence profile displays. And not only does the database cover naturally cyclic proteins, but has tools to help you design your own!

Conan K. L. Wang, Quentin Kaas, Laurent Chiche, and David J. Craik
CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
Nucleic Acids Research Advance Access published on November 5, 2007.

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