Molecular sterics guide tmRNA translocation on the ribosome

Translation of defective mRNA transcripts can lead to the formation of stalled ``non-stop'' ribosome complexes. To rescue these ribosomes, bacteria have evolved a mechanism called trans-translation that is mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). During the translocation step of trans-translation, the stalled mRNA is ejected and the reading frame found in the mRNA-like domain (MLD) of tmRNA is loaded into the mRNA channel. The ribosome then translates the new template, thereby tagging the nascent protein for degradation. While structures of tmRNA-SmpB on the ribosome have been available for years, little is known about the molecular factors that govern the dynamics of tmRNA translocation. Here, we use an energetically smooth model (i.e. SMOG) to simulate translocation of tmRNA-SmpB, which reveals that the structure of the ribosome gives rise to a preferred sequence of conformational substeps. Specifically, the tRNA-like domain (TLD) translocates, then the MLD loads, and finally the C-terminal tail of SmpB rearranges. These steps are interdependent and associated with a range of sterically-induced barriers that regulate the kinetics. This provides a structural and energetic framework for understanding, and ultimately controlling, the dynamics of trans-translation.