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Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation
Wu, SG; Li, LC; Li, Q; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu, Peoples R China.; Wu, SG (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing, Peoples R China.
2017
发表期刊BIOPHYSICAL JOURNAL
卷号112期号:11页码:2253-2260
文章类型Article
摘要In genetic transcription, molecular dynamic details and energetics of NTP binding to the active site of RNA polymerase (RNAP) are poorly understood. In this article, we investigated the NTP binding process in T7 RNAP using all-atom MD simulation combined with the umbrella sampling technique. Based on our simulations, a two-step mechanism was proposed to explain NTP binding: first, substrate NTP in aqueous solution, which carries a magnesium ion, diffuses through a secondary channel of RNAP to attain a pore region, where it undergoes conformational changes to give a correct orientation; next, the NTP establishes initial basepairing contacts with the template nucleoside (TN). Our free-energy calculations suggest that both steps are spontaneous. This mechanism can easily explain the problem of NTP binding with different orientations. Moreover, it is found that the nascent NTP:TN basepair is fragile and easily broken by thermal disturbance. Therefore, we speculate that the-fingers domain will-be triggered to close, so as to create a steady environment for the next chemical step. The observations from the work provide valuable information for comprehensively understanding the mechanism of the basic step in genetic transcription.
学科领域Biophysics
资助者National 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] ; National 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]
DOIhttp://dx.doi.org/10.1016/j.bpj.2017.04.039
关键词[WOS]PARTICLE MESH EWALD ; AMBER FORCE-FIELD ; MOLECULAR-DYNAMICS ; NUCLEIC-ACIDS ; TRANSLOCATION ; GROMACS ; MODEL
语种英语
资助者National 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] ; National 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]
WOS类目Biophysics
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/22038
专题理论物理所SCI论文
通讯作者Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu, Peoples R China.; Wu, SG (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing, Peoples R China.
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Wu, SG,Li, LC,Li, Q,et al. Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation[J]. BIOPHYSICAL JOURNAL,2017,112(11):2253-2260.
APA Wu, SG,Li, LC,Li, Q,Wu, SG ,&Wu, SG .(2017).Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation.BIOPHYSICAL JOURNAL,112(11),2253-2260.
MLA Wu, SG,et al."Mechanism of NTP Binding to the Active Site of T7 RNA Polymerase Revealed by Free-Energy Simulation".BIOPHYSICAL JOURNAL 112.11(2017):2253-2260.
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