Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome

J Phys Chem B. 2022 Oct 27;126(42):8447-8459. doi: 10.1021/acs.jpcb.2c05513. Epub 2022 Oct 17.

Abstract

Protein synthesis involves a complex series of large-scale 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 (aa-tRNA) 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-Å 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Peptidyl Transferases* / metabolism
  • Protein Biosynthesis
  • RNA, Transfer / chemistry
  • RNA, Transfer, Amino Acyl* / chemistry
  • RNA, Transfer, Amino Acyl* / genetics
  • RNA, Transfer, Amino Acyl* / metabolism
  • Ribosomes / chemistry

Substances

  • RNA, Transfer, Amino Acyl
  • Peptidyl Transferases
  • RNA, Transfer