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

	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
	Pang, Xueqin 1,2,3; Han, Keli 1; Cui, Qiang 2,3
刊名	journal of computational chemistry
	2013-07-15
卷号	34 期号:19 页码:1620-1635
关键词	DNA repair enzymes molecular dynamics non-heme iron crystal packing protein-DNA interaction
通讯作者	韩克利 ; cui qiang
产权排序	待补充
合作状况	英
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.
学科主题	物理化学
WOS标题词	science & technology ; physical sciences
类目[WOS]	chemistry, multidisciplinary
研究领域[WOS]	chemistry
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
收录类别	SCI
资助信息	1，1
原文出处	1635
语种	英语
WOS记录号	WOS:000320389700002
公开日期	2014-09-11
内容类型	期刊论文
源URL	[http://159.226.238.44/handle/321008/119209]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
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
推荐引用方式 GB/T 7714	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.
APA	Pang, Xueqin,Han, Keli,&Cui, Qiang.(2013).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.journal of computational chemistry,34(19),1620-1635.
MLA	Pang, Xueqin,et al."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".journal of computational chemistry 34.19(2013):1620-1635.