Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling

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	Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling
	Huang, Yan-Dong ; Shua, Jian-Wei ; Shuai JW(帅建伟)
刊名	http://dx.doi.org/10.1021/jp4021933
	2013
关键词	MOLECULAR-DYNAMICS SIMULATIONS INCLUDING CHARGE-TRANSFER AMYLOID-BETA-PEPTIDE ALZHEIMERS-DISEASE FORCE-FIELD ZINC-BINDING ENERGY AGGREGATION WATER IONS
英文摘要	National Natural Science Foundation of China [30970970]; China National Funds for Distinguished Young Scientists [11125419]; Funds for the Leading Talents of Fujian Province; Key Laboratory for Chemical Biology of Fujian Province, Xiamen University; Xiamen Super Computing Center; Zinc is found saturated in the deposited Amyloid-beta (A beta) peptide plaques in Alzheimer's disease (AD) patients' brains. Binding of zinc promotes aggregation of A beta, including the pathogenic aggregates. Up to now, only the region 1-16 of A beta complexed with zinc (A beta(1-16)-Zn) is defined structurally in experiment. In order to explore the induced polarization effect of zinc on the global fluctuations and the experimentally observed coordination mode of A beta(1-16)-Zn, we consider an all-atom molecular dynamics (MD) of A beta(1-16)-Zn solvated in implicit water. In our model, the zinc polarization affects the whole peptide. The induced dipoles are divided into three distinct scales according to their distances from zinc. Besides, the atomistic polarizability on the coordinating side chains is rescaled to describe the electron redistribution effect. We show that, associated with proper van der Waals (vdW) parameters, our model not only obtains the reasonable coordinating configuration of zinc binding site but also retains the global stabilization, especially the N-terminal region, of the A beta(1-16)-Zn. We suggest that it is the induced polarization effect that promotes reasonable solvent exposures of hydrophobic/hydrophilic residues regarding zinc-induced A beta aggregation.
语种	英语
出版者	AMER CHEMICAL SOC
内容类型	期刊论文
源URL	[http://dspace.xmu.edu.cn/handle/2288/91899]
专题	物理技术－已发表论文
推荐引用方式 GB/T 7714	Huang, Yan-Dong,Shua, Jian-Wei,Shuai JW. Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling[J]. http://dx.doi.org/10.1021/jp4021933,2013.
APA	Huang, Yan-Dong,Shua, Jian-Wei,&帅建伟.(2013).Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling.http://dx.doi.org/10.1021/jp4021933.
MLA	Huang, Yan-Dong,et al."Induced Dipoles Incorporated into All-Atom Zn Protein Simulations with Multiscale Modeling".http://dx.doi.org/10.1021/jp4021933 (2013).