Update on structures

First an update on the last one:
The structure of EF-Tu on the ribosome has now been solved with a non-hydrolyzable guanine nucleotide, in the true activated state. The metal ion that I guessed might be there is in fact not, but the ordered region of the effector loop is, in fact, ordered. This will hopefully lay to rest the idea that the elongation factors are activated by DISordering of their active site loops, which was always the biggest eyesore of all the models for their function so far. And the contacts with the ribosome are surprisingly simple, involving mainly just two histidines acting as a "ruler" to measure the orientation of the rRNA phosphate backbone. One is aligned in a phosphate-imidazole-water network vaguely reminiscent of the serine protease catalytic triad, explaining enhanced catalysis.

In addition, the number of G-protein coupled receptor structures has been steadily increasing. A friend asked me when I thought that solving new inactive GPCR structures would become boring, and while I'm sure this point will come sooner than anyone would predict at this time, we still have a ways to go. The family of seven-transmembrane receptors is very diverse, and there will no doubt be peculiarities to some of the more atypical members, like metabotropic glutamate receptors or even weirder ones like Frizzled. Yes, I know the last is not technically a GPCR, though it can be made into one quite easily by merely mutating loops, so I think of it as one. And that's not to mention the 100+ orphan receptors, whose ligand identification may be accelerated if we had structures.

A possible mechanism for elongation factors--finally?

Like the last speculation, this one involves the ribosome. In particular, the two elongation factors that in bacteria are known as EF-Tu and EF-G. Like all GTPases, these proteins have a catalytic domain that resembles the Ras family of signaling molecules. Clearly, however, the details of the catalysis are distinct. In common with each other, both types of proteins have low catalytic activity on their own (though the quantitative meaning of "low" varies"), and need to be activated by binding to something else in order to achieve rapid catalysis.

In the case of Ras-like proteins, these partners are called GTPase-activating proteins, or GAPs, and they bind to a particular region of the proteins near the phosphates of the bound GTP. Their activity commonly (though not always) involves an arginine side chain that is inserted into the active site and presumably stabilizes the transition state. However, EF-Tu and EF-G are activated by interacting with a particular state of the ribosome. The sarcin-ricin loop, or SRL, of the large subunit occupies a position similar to GAPs in Ras-like GTPases, but in the available structures it makes few contacts to the protein. This is probably due to the fact that one part of the protein, the so-called Switch I segment, is disordered.

Fold.it

Today I found an interesting site called Foldit, where you can download a program that lets you try folding a protein graphically. It differs from sites like Folding@home, which just draw on your computer's spare processor cycles, in that it actually hopes to use human intuition to help solve the protein folding problem, and compare it to the performance of computer algorithms on the same task. I downloaded it, and wanted to give my opinion on it.

Just a crazy idea (warning, technical)

This is officially the first time I actually say something "serious" about science on this blog. I don't know if there are any who will read this who will have the knowledge to even understand this, but I mainly want to record this somewhere in the off case that it turns out to be correct.

Anyway, I have had a long-standing interest in the ribosome, and recently I read a structural paper in Cell reporting the structure of the ribosome in complex with a ribonuclease called RelE. This is a heck of a weird RNase, as it cuts messenger RNA as it is being translated, in the middle of a codon that's about to be read.

The authors show very convincingly that the RNA is NOT cleaved between the first and second nucleotides of the codon, but that it is cleaved between the second and third nucleotide. In the structure, this site lines up with a site on RelE that corresponds to the active site in a number of related RNases, and that's all well and good.