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学科主题: 物理化学
题名: A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family
作者: Pang, Xueqin1, 2, 3;  Han, Keli1;  Cui, Qiang2, 3
通讯作者: 韩克利 ;  Cui qiang
关键词: DNA repair enzymes ;  molecular dynamics ;  non-heme iron ;  crystal packing ;  protein-DNA interaction
刊名: JOURNAL OF COMPUTATIONAL CHEMISTRY
发表日期: 2013-07-15
DOI: 10.1002/jcc.23305
卷: 34, 期:19, 页:1620-1635
收录类别: SCI
合作性质: 
文章类型: Review
部门归属: 11
项目归属: 1101
产权排名: 待补充
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Multidisciplinary
资助者: 1,1
研究领域[WOS]: Chemistry
英文摘要: To facilitate computational study of proteins in the AlkB family and related -ketoglutarate/Fe(II)-dependent dioxygenases, we have tested a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard-Jones parameters. Calculations for an AlkB active site model in the gas phase and approximate to 150 ns molecular dynamics (MD) simulations for two enzyme-dsDNA complexes (E. coli AlkB-dsDNA and ABH2-dsDNA) suggest that this simple modeling strategy provides a satisfactory description of structural properties of the Fe(II) site in AlkB enzymes, provided that care is exercised to control the binding mode of carboxylate (Asp) to the iron. MD simulations using the model for AlkB-dsDNA and ABH2-dsDNA systems find that although the structural features for the latter are overall in good agreement with the crystal structure, the dsDNA, and AlkB-dsDNA interface undergo substantial changes during the MD simulations from the crystal structure. Even for ABH2, new interactions form between a long loop region and dsDNA upon structural relaxation of the loop, supporting the role of this loop in DNA binding despite the lack of interactions between them in the crystal structure. Analysis of DNA backbone torsional distributions helps identify regions that adopt strained conformations. Collectively, the results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes; the simulations also provide additional insights regarding why AlkB and ABH2 prefer single-strand and double-strand DNA, respectively, as substrate. (c) 2013 Wiley Periodicals, Inc.
关键词[WOS]: GENOME-WIDE ASSOCIATION ;  NUCLEIC-ACID STRUCTURES ;  OBESITY-ASSOCIATED FTO ;  DNA ALKYLATION DAMAGE ;  REPAIR ENZYME ALKB ;  MOLECULAR-DYNAMICS ;  CRYSTAL-STRUCTURES ;  OXIDATIVE DEMETHYLATION ;  ESCHERICHIA-COLI ;  MAMMALIAN DNA
语种: 英语
原文出处: 查看原文
WOS记录号: WOS:000320389700002
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/119209
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Liaoning, Peoples R China
2.Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
3.Univ Wisconsin, Inst Theoret Chem, Madison, WI 53706 USA

Recommended Citation:
Pang, Xueqin,Han, Keli,Cui, Qiang. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2013,34(19):1620-1635.
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