Monday, September 21, 2009

The first peptide bond. EF-P and Ratcheting

In the third week of August Steitz and collaborators at Yale publish in science the crystallographic structures of the T. Thermophilus ribosome with Elongation Factor P (EF-P) bound to it. Also initiator tRNA and mRNA are included in the crystal.
"The essential role of EF-P in the cell may be to correctly position the fMet-tRNAifMet in the P site for the first step of peptide bond formation by making several interactions with the backbone of the tRNA."

Science 325, 909-1032, 2009

An article in the same volume of Science by Cate et al. at Berkeley, shows the crystallographic results of catching the ribosome of e. coli in intermediate states of ratcheting which "provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation."
"Positioning of tRNA on the ribosome is proposed to occur through a ratcheting mechanism. Central to this mechanism is a rotation of the small ribosomal subunit relative to the large subunit (see Figure) that occurs in all stages of translation—initiation, elongation, termination, and ribosome recycling"

Science 325, 1014-1017, 2009

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Thursday, September 10, 2009

Yet another interesting RNA (anti-NF-(kappa)B RNA aptamer)

Whereas in DNA you have a quite small set of possible structures, ranging from A-form to Z-form, in RNA there's a whole ZOO of possibilities. The one I ran upon this week has a difficult name:
anti-NF-(kappa)B RNA aptamer
The whole idea of what this aptamer seems to be doing is to mimic the B-form of DNA, which RNA rarely manages to attain. Of course, this so called mimicry is obtained in the backbone, which, of course, determined the width of the grooves, which are the most common mechanism which nucleic acids use for their recognition of other molecules inside the cell.
It's quite interesting how three guanines stack in top of each other, two are from the same side of the strand, and one is from the opposite side of the strand, as can easily be seen in the following figure.

The work was carried out by Nicholas J. Reiter, James Maher III, and Samuel E. Butcher at Wisconsin, published in NAR, 36, 1227-1236, 2008