Structural insights into cognate versus near-cognate discrimination during decoding

Structural Biology Unit, CIC-bioGUNE, Derio, Basque Country, Spain.
The EMBO Journal (Impact Factor: 10.43). 03/2011; 30(8):1497-507. DOI: 10.1038/emboj.2011.58
Source: PubMed


The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) 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 TC 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 elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. 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 on how the conformational signals conveyed to the GTPase differ in the two cases.

Download full-text


Available from: Eduard Schreiner
  • Source
    • "Thus a molecular spring like mechanism is deciphered by the cryo-EM study during the tRNA selection and accommodation process. Furthermore, a very recent cryo-EM study (Agirrezabala et al. 2011 ) based on the analyses of the 70S⋅TC complexes containing a near-cognate aa-tRNA, in addition to its cognate counterpart, observed distinct structural changes, which indicates an induced fi t mechanism during aa-tRNA incorporation. The atomic details of some of the above fi ndings have been con fi rmed by the crystal structures of different 70S⋅TC complexes (Schmeing et al. 2009 ; Voorhees et al. 2010 ) . "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ribosome is a complex macromolecular machine responsible for the protein synthesis in all living organisms. During protein synthesis ribosome interacts with several translation factors and undergoes extensive conformational changes which are integral part of the translation process. Cryo-Electron Microscopy with powerful image-processing software has contributed immensely for elucidating those dynamic structural events; thereby our understanding on the intricate mechanisms of the translation process has advanced significantly. Understanding translation process and the mechanisms of the ribosomal functions are fundamental to our existence. In this chapter, we briefly discussed the cryo-EM process and its application on the translation research and highlighted many of the exciting findings revealed through it.
    Full-text · Chapter · Jan 2013
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Accurate electrostatic descriptions of aqueous solvent are critical for simulation studies of bio-molecules, but the computational cost of explicit treatment of solvent is very high. A computationally more feasible alternative is a generalized Born implicit solvent description which models polar solvent as a dielectric continuum. Unfortunately, the attainable simulation speedup does not transfer to the massive parallel computers often employed for simulation of large structures. Longer cutoff distances, spatially heterogenous distribution of atoms and the necessary three-fold iteration over atom-pairs in each timestep combine to challenge efficient parallel performance of generalized Born implicit solvent algorithms. Here we report how NAMD, a parallel molecular dynamics program, meets the challenge through a unique parallelization strategy. NAMD now permits efficient simulation of large systems whose slow conformational motions benefit most from implicit solvent descriptions due to the inherent low viscosity. NAMD's implicit solvent performance is benchmarked and then illustrated in simulating the ratcheting Escherichia coli ribosome involving ~250,000 atoms.
    Preview · Article · Nov 2011 · Journal of Chemical Theory and Computation
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Transfer RNAs (tRNAs) are ancient molecules whose origin goes back to the beginning of life on Earth. Key partners in the ribosome-translation machinery, tRNAs read genetic information on messenger RNA and deliver codon specified amino acids attached to their distal 3'-extremity for peptide bond synthesis on the ribosome. In addition to this universal function, tRNAs participate in a wealth of other biological processes and undergo intricate maturation events. Our understanding of tRNA biology has been mainly phenomenological, but ongoing progress in structural biology is giving a robust physico-chemical basis that explains many facets of tRNA functions. Advanced sequence analysis of tRNA genes and their RNA transcripts have uncovered rules that underly tRNA 2D folding and 3D L-shaped architecture, as well as provided clues about their evolution. The increasing number of X-ray structures of free, protein- and ribosome-bound tRNA, reveal structural details accounting for the identity of the 22 tRNA families (one for each proteinogenic amino acid) and for the multifunctionality of a given family. Importantly, the structural role of post-transcriptional tRNA modifications is being deciphered. On the other hand, the plasticity of tRNA structure during function has been illustrated using a variety of technical approaches that allow dynamical insights. The large range of structural properties not only allows tRNAs to be the key actors of translation, but also sustain a diversity of unrelated functions from which only a few have already been pinpointed. Many surprises can still be expected.
    Full-text · Article · Jan 2012 · WIREs RNA
Show more