Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme

• 来源期刊: 中国物理B（英文版）
• 关键词: RNA polymerase molecular dynamics simulation molecular motor Brownian ratchet
• 年，卷（期）: 2017,（3）
• 页码范围: 195-206
• 页数: 12页
• 语种: 英文
• DOI: 10.1088/1674-1056/26/3/030201

摘要

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 intemal potential of the enzyme itself generates a small difference in free energy (AE) between the post-and pre-translocation positions of Tyr639.The calculated value of AE 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 AE arising from the conformational change of the enzyme itself.