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

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.

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► Atomic models confirm assignments of previous FRET studies of L1 stalk dynamics.
► Compared to elongator tRNA-Phe, tRNA-fMet binds deeper into the 30S P site.
► Compared to elongator tRNA-Phe, tRNA-fMet interacts less strongly with the L1 stalk.
► Simulation suggests that L1 stalk opening is involved in tRNA release.