Model of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations

Ishida, Hisashi; Matsumoto, Atsushi

To understand the mechanism of reverse tRNA translocation, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the pre-translocational states by fitting the complex into cryo-EM density maps. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The results indicate that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gatet. Conformational change of EF-G was interpreted as the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion.