Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome

Protein synthesis involves a complex series of largescale conformational changes in the ribosome. While long-lived intermediate states of these processes can be characterized by experiments, computational methods can be used to identify the interactions that contribute to the rate-limiting free-energy barriers. To this end, we use a simplified energetic model to perform molecular dynamics (MD) simulations of aminoacyl-tRNA (aatRNA) accommodation on the ribosome. While numerous studies have probed the energetics of the early stages of accommodation, we focus on the final stage of accommodation, where the 3 '-CCA tail of aa-tRNA enters the peptidyl transferase center (PTC). These simulations show how a distinct intermediate is induced by steric confinement of the tail, immediately before it completes accommodation. Multiple pathways for 3 '-CCA tail accommodation can be quantitatively distinguished, where the tail enters the PTC by moving past a pocket enclosed by Helix 89, 90, and 92, or through an alternate route formed by Helix 93 and the P-site tRNA. C2573, located within Helix 90, is shown to provide the largest contribution to this late-accommodation steric barrier, such that sub-angstrom perturbations to this residue can alter the time scale of tail accommodation by nearly an order of magnitude. In terms of biological function, these calculations suggest how this late-stage sterically induced barrier may contribute to tRNA proofreading by the ribosome.

Automated summary

Protein synthesis involves complex conformational changes in the ribosome, and this study focuses on the final stage of accommodation of aminoacyl-tRNA on the ribosome. By using molecular dynamics simulations, it was discovered that a distinct intermediate is induced by steric confinement of the 3'-CCA tail of aa-tRNA before it completes accommodation. Multiple pathways for the tail accommodation were found, with one pathway involving Helix 89, 90, and 92, and another involving Helix 93 and the P-site tRNA. Additionally, the study identified that C2573 in Helix 90 plays a significant role in the steric barrier of late-stage accommodation.