The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle

Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha, Zaida Luthey-Schulten, K. Schulten

Research output: Contribution to journalArticle

Abstract

The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNAfMet interacts less strongly with the L1 stalk compared to elongator tRNAPhe, as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.

Original languageEnglish (US)
Pages (from-to)741-760
Number of pages20
JournalJournal of Molecular Biology
Volume402
Issue number4
DOIs
StatePublished - Oct 2010

Keywords

  • Flexible fitting
  • FRET
  • MDFF
  • Modified ribonucleosides
  • Translocation

ASJC Scopus subject areas

  • Molecular Biology

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    Trabuco, L. G., Schreiner, E., Eargle, J., Cornish, P., Ha, T., Luthey-Schulten, Z., & Schulten, K. (2010). The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle. Journal of Molecular Biology, 402(4), 741-760. https://doi.org/10.1016/j.jmb.2010.07.056