中国物理B ›› 2017, Vol. 26 ›› Issue (3): 30201-030201.doi: 10.1088/1674-1056/26/3/030201

• GENERAL •    下一篇

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

Zhan-Feng Wang(王展峰), Zhi-Qiang Zhang(张志强), Yi-Ben Fu(付一本), Peng-Ye Wang(王鹏业), Ping Xie(谢平)   

  1. Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • 收稿日期:2016-10-24 修回日期:2016-11-21 出版日期:2017-03-05 发布日期:2017-03-05
  • 通讯作者: Ping Xie E-mail:pxie@aphy.iphy.ac.cn
  • 基金资助:

    Project supported by the National Natural Science Foundation of China (Grant Nos. 11374352 and 11274374) and the National Key Research and Development Program of China (Grant No. 2016YFA0301500).

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

Zhan-Feng Wang(王展峰), Zhi-Qiang Zhang(张志强), Yi-Ben Fu(付一本), Peng-Ye Wang(王鹏业), Ping Xie(谢平)   

  1. Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • Received:2016-10-24 Revised:2016-11-21 Online:2017-03-05 Published:2017-03-05
  • Contact: Ping Xie E-mail:pxie@aphy.iphy.ac.cn
  • Supported by:

    Project supported by the National Natural Science Foundation of China (Grant Nos. 11374352 and 11274374) and the National Key Research and Development Program of China (Grant No. 2016YFA0301500).

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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 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.

关键词: RNA polymerase, molecular dynamics simulation, molecular motor, Brownian ratchet

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.

Key words: RNA polymerase, molecular dynamics simulation, molecular motor, Brownian ratchet

中图分类号:  (Molecular dynamics and particle methods)

  • 02.70.Ns
05.40.-a (Fluctuation phenomena, random processes, noise, and Brownian motion) 05.40.Jc (Brownian motion) 87.15.kj (Protein-polynucleotide interactions)