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题名: Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations
作者: Wu, SG ;  Jiang, MQ ;  Liu, L
刊名: COMPUTATIONAL AND THEORETICAL CHEMISTRY
出版日期: 2016
卷号: 1094, 页码:127-132
关键词: Molecular dynamics simulation ;  T7 RNA polymerase ;  PPi release ;  Potential of mean force
学科分类: Chemistry
DOI: http://dx.doi.org/10.1016/j.comptc.2016.09.005
通讯作者: Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.
文章类型: Article
英文摘要: In this article, we explored pyrophosphate ion (PPi) release mechanism in T7 RNAP using all-atom free energy simulations in explicit solvent. Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) methods were combined to estimate the potential of mean force (PMF) for the PPi release in T7 RNAP. PPi is a small group with negative charges. After binding a Mg2+ ion, the formed (Mg-PPi)(2-) complex is able to bind with both positively and negatively charged groups. Our simulation results show there is a large free energy barrier in the PMF profile for PPi release. Non-bonded interaction analysis suggests that the PPi is firmly trapped in the pore region of the secondary channel, which is composed of many polar, negatively and positively charged groups. Strong electric interactions from the surrounding groups contribute mostly to the high energy barrier for PPi release. Hydrogen bond map clearly exhibits part of the interaction network that the PPi has been trapped in. Therefore, we conclude that PPi is less likely to be released spontaneously. Additional energy input is needed to facilitate this process. It is deduced that NTP addition reaction may serve as an energy provider to drive PPi release. Then the whole NAC mechanism can be well explained. It is expected that our study provides a clear picture on the essential step of RNA transcription at atom-level resolution. (C) 2016 Elsevier B.V. All rights reserved.
类目[WOS]: Chemistry, Physical
关键词[WOS]: PARTICLE MESH EWALD ;  MOLECULAR-DYNAMICS ;  TRANSLOCATION ;  DNA
收录类别: SCI
项目资助者: National Natural Science Foundation of China [11405113] ;  Science and Technology Plan of Sichuan Province, China [2010JY0122]
语种: 英语
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/21505
Appears in Collections:理论物理所2016年知识产出_期刊论文

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Recommended Citation:
Wu, SG,Jiang, MQ,Liu, L. Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations[J]. COMPUTATIONAL AND THEORETICAL CHEMISTRY,2016,1094:127-132.
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