2012 Fiscal Year Final Research Report
Analysis of conformational changes in ribosome during protein synthesis reaction cycle
| Project/Area Number |
22570165
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Japan Atomic Energy Agency |
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Principal Investigator |
ISHIDA Hisashi 独立行政法人日本原子力研究開発機構, 量子ビーム応用研究部門, 研究副主幹 (60360418)
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| Project Period (FY) |
2010 – 2012
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| Keywords | リボソーム / 電子顕微鏡 / 分子動力学 / 伸長因子EF-G / tRNA 転位 |
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| Research Abstract |
To understand the mechanism of reverse tRNA translocation in ribosome, all-atom molecular dynamics simulations of ribosome-mRNA-tRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers : one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which triggered P-tRNA to move over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which located the two tRNAs in the hybrid state. 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. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with the A/P-tRNA.
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