Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

The Mechanism of aa-tRNA Entry into the Ribosome

The selection process of aminoacyl-tRNAs (aa-tRNAs) starts with the entry of the ternary complex formed by aa-tRNA, elongation factor Tu (EF-Tu) and GDP into the ribosome, placing the aa-tRNA in the A/T position, with a distorted conformation compared to the A-site tRNA (3-8). The distortion, visible by cryo-EM in a kirromycin-stalled E. coli A/T ribosome complex after GTP hydrolysis, has been recognized as essential for probing initial codon-anticodon recognition (2, 7). However, the origin of the conformational deformation was interpreted differently in different studies. Valle et al (7) modeled the distortion as a kink at the junction between the D and anticodon stems (later confirmed by molecular dynamics flexible fitting. MDFF) (5, 8), and proposed that it was triggered by the interaction of aa-tRNA with helix 69 of the 23S rRNA, but this proposal was weakened by the discovery that ribosomes with helix 69 deleted still translate with virtually unchanged fidelity (1; R. Greene, personal communication). Recently, Schuette et al. (3), analyzing a kirromycin-stalled T. Thermophilus A/T ribosome complex by rigid-body fitting, described the observed distortion of the aa-tRNA as a twist between the T and acceptor stems, as well as opening between the T-acceptor arm and D stem. These authors postulated that there is no ribosome-induced conformational change prior to codon-anticodon interaction, and suggested that a nearly correct steric engagement in the initial approach might result from conformational fluctuations of the tRNA. We now address this question by molecular dynamics simulations on a free Phe-tRNA·EF-Tu complex. These simulations show that aa-tRNA in the context of the ternary complex has a dynamic behavior distinct from a free aa-tRNA. The conformational distortion in the D loop and the anticodon stem loop occurs in a much larger and diverse range, compared with free aa-tRNA, when the aa-tRNA is bound with EF-Tu. It includes a pronounced mode of bending/twisting in the region identified by Valle et al. (7), toward a conformation that readily facilitates codon-anticodon contact. Our present results demonstrate that EF-Tu-bound aa-tRNA may spontaneously (within a time frame commensurate with physiological requirements) form a geometry permitting codon-anticodon interaction, in agreement with Schuette et al.?s hypothesis.

References and Footnotes
  1. Ali IK et al. Deletion of a central ribosomal intersubunit RNA bridge. Molecular Cell 23, 865-874 (2006).
  2. Frank J et al. The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Lett 579: 959?962 (2005).
  3. Schuette JC et al. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J. 28: 755-765 (2009).
  4. Stark H et al. Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nat Struct Biol 9: 849?854 (2002).
  5. Trabucco L et al. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics. Structure 16: 673-683 (2008).
  6. Valle et al. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21: 3557-3567 (2002).
  7. Valle M et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol 10: 899?906 (2003).
  8. Villa E et al. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci USA. 106: 1063-1068 (2009).

Wen Li1
Elizabeth Villa2
Joachim Frank1, 3, 4

3Howard Hughes Medical Institute
1Department of Biochemistry and Molecular Biophysics
Columbia University, 650 W. 168th Street, BB2-221
New York NY 10032
2Max Planck Institute of Biochemistry
D-82152 Martinsried, Germany
4Department of Biological Sciences
Columbia University

ph: 212 305-9510
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email Joachim Frank