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Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha, Zaida Luthey-Schulten, and Klaus Schulten. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Journal of Molecular Biology, 402:741-760, 2010.

TRAB2010A 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 through the molecular dynamics flexible fitting method data from cryoelectron microscopy, X-ray crystallography, and molecular dynamics simulations, atomic models of tRNAs in the hybrid P/E state interacting with the L1 stalk are obtained that confirm the assignment of FRET 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 than elongator tRNAs, 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 to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.


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