An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

doi:10.1088/1674-1056/26/10/100203

中国物理B ›› 2017, Vol. 26 ›› Issue (10): 100203-100203.doi: 10.1088/1674-1056/26/10/100203

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

Zhan-Feng Wang(王展峰), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业), Ping Xie(谢平)

Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China

收稿日期:2017-04-17 修回日期:2017-07-08 出版日期:2017-10-05 发布日期:2017-10-05
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 11674381) and the National Key Research and Development Program of China (Grant No. 2016YFA0301500).

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

Zhan-Feng Wang(王展峰), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业), Ping Xie(谢平)

Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing 100190, China

Received:2017-04-17 Revised:2017-07-08 Online:2017-10-05 Published:2017-10-05
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 11674381) and the National Key Research and Development Program of China (Grant No. 2016YFA0301500).

摘要/Abstract

摘要：

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre-and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre-and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson-Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA-RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP.

关键词: RNA polymerase, transcription elongation, fidelity control, molecular dynamics simulation

Abstract:

Key words: RNA polymerase, transcription elongation, fidelity control, molecular dynamics simulation

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)

王展峰, 刘玉如, 王鹏业, 谢平. An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection[J]. 中国物理B, 2017, 26(10): 100203-100203.

Zhan-Feng Wang(王展峰), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业), Ping Xie(谢平). An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection[J]. Chin. Phys. B, 2017, 26(10): 100203-100203.

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An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

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