Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme |
| |
| Affiliation: | Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China |
| |
| Abstract: | T7 RNA polymerase can transcribe DNA to RNA by translocating along the DNA. Structural studies suggest that the pivoting rotation of the O helix in the fingers domain may drive the movement of the O helix C-terminal Tyr639 from pre- to post-translocation positions. In a series of all-atom molecular dynamics simulations, we show that the movement of Tyr639 is not tightly coupled to the rotation of the O helix, and that the two processes are only weakly dependent on each other. We also show that the internal potential of the enzyme itself generates a small difference in free energy (ΔE) between the post- and pre-translocation positions of Tyr639. The calculated value of ΔE is consistent with that obtained from single-molecule experimental data. These findings lend support to a model in which the translocation takes place via a Brownian ratchet mechanism, with the small free energy bias ΔE arising from the conformational change of the enzyme itself. |
| |
| Keywords: | RNA polymerase molecular dynamics simulation molecular motor Brownian ratchet |
| 本文献已被 CNKI 等数据库收录！ |
| 点击此处可从《中国物理 B》浏览原始摘要信息 |
|
点击此处可从《中国物理 B》下载免费的PDF全文 |
|
