In a recent work published by the EMBO Journal, images of the ribosome bound to either a cognate or a near-cognate tRNA were obtained by cryo-electron microscopy, and MDFF was employed to generate atomic models, shedding light into the mechanisms by which the ribosome discriminates between correct and incorrect tRNAs. The work is a collaboration between the Schulten (University of Illinois at Urbana-Champaign, USA) and the Frank (Columbia University, USA) groups.
Structural insights into cognate vs. near-cognate discrimination during decoding.
Xabier Agirrezabala, Eduard Scheiner, Leonardo G. Trabuco, Jianlin Lei, Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank. EMBO J., 30, 1497-1507, 2011.
The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with (UGA/stop) codons and incubated with ternary complex containing the near-cognate Trp-tRNA{Trp} in the presence of kirromycin. Going through more than 350,000 images and employing image classification procedures, we find 8% in which the ternary complex is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to EF-Tu and the ribosome, as well as the domain movements of the ribosome. The data bring direct structural insights into the induced fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues as to how the conformational signals conveyed to the GTPase differ in the two cases.
