The role of L1 stalk-tRNA interaction in the ribosome elongation cycle

J Mol Biol. 2010 Oct 1;402(4):741-60. doi: 10.1016/j.jmb.2010.07.056. Epub 2010 Aug 5.


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 tRNA(fMet) interacts less strongly with the L1 stalk compared to elongator tRNA(Phe), 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Peptide Chain Elongation, Translational*
  • Protein Biosynthesis
  • RNA, Transfer / chemistry
  • RNA, Transfer / metabolism*
  • RNA, Transfer, Met
  • RNA, Transfer, Phe
  • Ribosomes / chemistry
  • Ribosomes / metabolism*


  • RNA, Transfer, Met
  • RNA, Transfer, Phe
  • RNA, Transfer