ITP OpenIR  > 理论物理所2017年知识产出
Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription
Wu, SG; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
2017
发表期刊PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷号85期号:6页码:1002-1007
文章类型Article
摘要Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PPi)? This problem still remains obscure. In this work, we studied the problem using all-atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PPi than the whole protein. Hence, PPi release is less likely to take it away. The other one forms tighter contacts with PPi relative to the protein. The formed (Mg2+-PPi)(2-) complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PPi release and guarantees a reasonable Mg2+ ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. (C) 2017 Wiley Periodicals, Inc.
关键词Molecular Dynamics Simulation T7 Rna Polymerase Magnesium Ion Transcription Mechanism Free Energy
学科领域Biochemistry & Molecular Biology ; Biophysics
资助者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] ; 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]
DOIhttp://dx.doi.org/10.1002/prot.25268
关键词[WOS]PARTICLE MESH EWALD ; RESIDUE ; GROMACS
语种英语
资助者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] ; 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]
WOS类目Biochemistry & Molecular Biology ; Biophysics
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/22047
专题理论物理所2017年知识产出
通讯作者Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
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Wu, SG,Wu, SG . Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2017,85(6):1002-1007.
APA Wu, SG,&Wu, SG .(2017).Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,85(6),1002-1007.
MLA Wu, SG,et al."Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 85.6(2017):1002-1007.
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