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

doi:10.1088/1674-1056/26/3/030201

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

Received: 24 October 2016
Revised: 21 November 2016
Accepted manuscript online:

PACS:	02.70.Ns	(Molecular dynamics and particle methods)
	05.40.-a	(Fluctuation phenomena, random processes, noise, and Brownian motion)
	05.40.Jc	(Brownian motion)
	87.15.kj	(Protein-polynucleotide interactions)

Fund:

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).

Corresponding Authors: Ping Xie
E-mail: pxie@aphy.iphy.ac.cn

Cite this article:

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) Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme 2017 Chin. Phys. B 26 030201

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

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