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Wu, SG; Jiang, MQ; Liu, L; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.
Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations
Source PublicationCOMPUTATIONAL AND THEORETICAL CHEMISTRY
Language英语
KeywordMolecular Dynamics Simulation T7 Rna Polymerase Ppi Release Potential Of Mean Force
AbstractIn 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.
2016
Volume1094Pages:127-132
Subject AreaChemistry
DOIhttp://dx.doi.org/10.1016/j.comptc.2016.09.005
Indexed BySCI
Funding OrganizationNational Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122]
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/21505
Collection理论物理所科研产出_SCI论文
Corresponding AuthorWu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.
Recommended Citation
GB/T 7714
Wu, SG,Jiang, MQ,Liu, L,et al. Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations[J]. COMPUTATIONAL AND THEORETICAL CHEMISTRY,2016,1094:127-132.
APA Wu, SG,Jiang, MQ,Liu, L,&Wu, SG .(2016).Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations.COMPUTATIONAL AND THEORETICAL CHEMISTRY,1094,127-132.
MLA Wu, SG,et al."Mechanism of pyrophosphate ion release in T7 RNA polymerase revealed by free energy simulations".COMPUTATIONAL AND THEORETICAL CHEMISTRY 1094(2016):127-132.
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