Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome

Abstract

Translocation of tRNA through the ribosome is essential for protein synthesis and for maintaining the open reading frame of mRNA translation. Translocation is associated with two large-scale rearrangements within the ribosome: an intersubunit rotation of the small subunit relative to the large subunit (rotation); and an intrasubunit rotation of small subunit head relative to its body (head swivel). Recent single-molecule FRET studies (smFRET) suggested that exaggerated head swivel motions accompany the translocation reaction coordinate. Here, we integrate molecular dynamics simulations of the 70S ribosome translocation complex with single molecule FRET studies to more fully characterize the conformational changes in the ribosome accompanying translocation, and the transit of key intermediates that have recently been identified by structural and smFRET investigations. By explicitly incorporating FRET labels into the simulations, we obtain configurations of the ribosome highly consistent with measured FRET efficiencies for each translocation intermediate. We find that a larger amplitude head swivel configuration (‘super swivel’) satisfies the constraints of FRET efficiency and conformational changes predicted to accompany translocation. In so doing, our study supports a simplified translocation pathway consistent with extant structural data and the order of events during and the geometric constraints predicted by recent smFRET initiatives. Our simulations also characterize the influence of dye flexibility on the smFRET distance estimates.