Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription

doi:http://dx.doi.org/10.1002/prot.25268

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	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.
刊名	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
	2017
卷号	85 期号:6 页码:1002-1007
关键词	Molecular Dynamics Simulation T7 Rna Polymerase Magnesium Ion Transcription Mechanism Free Energy
DOI	http://dx.doi.org/10.1002/prot.25268
英文摘要	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.
学科主题	Biochemistry & Molecular Biology ; Biophysics
语种	英语
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/22047]
专题	理论物理研究所_理论物理所1978-2010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.
推荐引用方式 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.