Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations

電子顕微鏡像と分子動力学シミュレーションを用いて解析されたリボソーム内tRNA転位の自由エネルギー地形

石田 恒; 松本 淳

Ishida, Hisashi; Matsumoto, Atsushi

To understand the mechanism of tRNA translocation in ribosome, all-atom molecular dynamics simulations of reverse translocation were carried out. Ribosome-tRNAs-mRNA-EFG complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Multistep structural changes, such as a ratchet-like motion between the small and large ribosomal subunits and rotation of the head of the small subunit were observed during translocation. onformational change of EF-G was interpreted as the result of the combination of the internal and external motions: the internal hinge-bending motion around axes from one subunit to the other, and external rotational motion triggered by L12 around an axis passing near the sarcin-ricin loop. These motions contributed to the extension of domain IV of EF-G to maintain its interaction with the A/P-tRNA during tRNA translocation.