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Wu, SG; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription
Source PublicationPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Language英语
KeywordMolecular Dynamics Simulation T7 Rna Polymerase Magnesium Ion Transcription Mechanism Free Energy
AbstractTwo 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.
2017
Volume85Issue:6Pages:1002-1007
Subject AreaBiochemistry & Molecular Biology ; Biophysics
DOIhttp://dx.doi.org/10.1002/prot.25268
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/311006/22047
CollectionSCI期刊论文
Corresponding AuthorWu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610066, Peoples R China.
Recommended Citation
GB/T 7714
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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