Thursday, December 20, 2007

Transmembrane pump structure

We are clearly now fully in the era of the membrane protein crystal structure--it's clear that even being in the greasy environment of the cell membrane isn't going to protect proteins much longer from the X-ray beams of determined structural biologists. This time, the structure is of the sodium potassium pump, also known as the Na+/K+ ATPase, which sets up the sodium and potassium gradients necessary for numerous cellular functions, from simple maintenance of osmotic balance to uptake of nutrients and nerve impulse transmission. Pharmacologically speaking, this protein is also the target of the simultaneously highly toxic and medically useful cardiac glycosides.

I am not nearly as surprised at the publication of this structure as I was at the adrenoceptor structure mentioned in my last post, or the structure of the amino acid transporter LeuT mentioned on here over a year ago, since multiple structures of a functionally very similar ion pump, namely the sarcoplasmic/endoplasmic reticulum Ca2+ ATPase, had been published years ago (interestingly, some newer structures of this Ca2+ ATPase were just released as well).

I skimmed through the paper in which the Na+/K+ ATPase structure is described, and curiously the authors make absolutely no mention of the cardiac glycoside binding site, despite the fact that there is a clearly visible pocket among the amino acid side chains known to be involved in the binding of these inhibitors. Maybe, a discussion of this site was omitted either due to the modest resolution (3.5 A), and/or because the K+ occupied form of the protein, which is (assumed to be) mimicked by the rubidium ions in the crystal structure, is known to have a lower affinity for cardiac glycosides than the unoccupied form. It seems to me that groups like Qiu et. al. were very much on the right track, though.

Friday, October 26, 2007

Shout it from the rooftops...

... a new G-protein coupled receptor (GPCR) has been crystallized!!! This one is actually pharmacology relevant, and closely homologous to the targets of many clinically important drugs. Namely, it's the beta2 adrenoceptor, bound to the partial inverse agonist ("beta blocker") carazolol. Immediately following a publication of the structure of the receptor complexed with carazolol and an antibody at modest (3.4 A in the plane of the membrane, 3.7 A along an axis normal to this plane) resolution in Nature, Brian Kobilka and colleagues published a high (2.4 A) resolution structure obtained by insertion of T4 lysozyme into the third intracellular loop, which yielded better-diffracting crystals. Congratulations to the Kobilka lab!

Those who have any kind of interest in structure-based drug design will most undoubtedly know how big this news is without me spouting all kinds of hype, and most others probably don't care anyway, so I won't give a long explanation. If you would like some more introduction, Keith Robison at Omics!, Omics! has a post on this. Any pharmacology or structural biology bloggers who actually read this should feel free to link here, write their own post if they think mine sucks, or of course can link directly to the articles as I have done.

The structures are not available from the PDB yet, and I haven't even examined the figures in the paper with the high resolution structure yet (beyond the new Kobilka lab front page graphic, which I just stumbled upon)--I want to see how much I can predict before I actually view the structure in detail. Nevertheless, once they are, I (and undoubtedly dozens of others) will be creating new models of other adrenoceptor complexes, as well as of other receptors in the amine subfamily. It is almost certain that these will be substantially more correct than the previous rhodopsin-based models, however illuminating the latter have been (and what I know about the new structure seems to say that they were not THAT far off).

...Whew! I haven't blogged in over five months, but I just had to say something about this. After a week that started with the southern California wildfires (I didn't have to evacuate, but I was close enough to see the smoke, and the campus has been closed), I receive notice of this. If someone had asked me last week to make a bet, I would have said I would have finished grad school before a drug-bound GPCR structure was published ( I just started this fall--note also that my area of grad study has nothing to do with GPCRs, crystallography, or pharmacology--this is just a personal area of interest). On the other hand, the structure of LeuT a little over two years ago totally caught me off guard too. I guess we're finally coming into the era of the membrane protein crystal structure. Any guesses as to when the first GPCR agonist complex structure will be published?