Balanced Interactions between Ribosomal Subunits Allow Rapid Large-Scale Rotation

Abstract

The ribosome consists of two subunits which remain associated through intersubunit bridges during tRNA translocation, despite large-scale rotations of the small 30S relative to the large 50S subunit. Stable ribosomes undergoing rapid rotation require the subunit binding free energy to be sufficiently strong and constant for different rotation angles. Here we investigate how this is achieved considering the large shifts the intersubunit bridges experience in particular at the periphery of the rotational movement. Using molecular dynamics simulations of x-ray structures refined against cryo-EM maps of the ribosome in 13 intermediate states of spontaneous translocation, we study the dynamics and energetics of the intersubunit contact network. To that aim, residues were grouped into clusters based on their observed intersubunit contacts. In addition to the central contact clusters, strong continuous interactions were also found for peripheral clusters. This continuity is realized by changing contact partners in the course of rotation. The most peripheral B1 bridges are stabilized by a changing pattern of contacts between residues of opposite charge that adapt to the rotational state. Continuous contacts of the strong B4 bridge are ensured by the flexibility of H34 helix (50S subunit) which follows the rotational movement and contacts multiple positively charged arginines on the 30S protein S15. The tRNAs which span the two subunits add to an almost constant degree to the intersubunit binding enthalpy, despite their very different positions in the ribosome. These mechanisms keep the strength of intersubunit interaction similar for different rotation angles allowing rapid rotation.