QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

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	QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface
	Yang ZY(杨振宇); Zhao YP(赵亚溥)
刊名	Materials Science and Engineering A-Structural Materials Properties Microstructure and Processing
	2006
通讯作者邮箱	yzhao@lnm.imech.ac.cn
ISSN号	0921-5093
通讯作者	Zhao, YP (reprint author), Chinese Acad Sci, Inst Mech, State Key Lab Nonlinear Mech, Beijing 100080, Peoples R China.
中文摘要	The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.
学科主题	力学
类目[WOS]	Nanoscience & Nanotechnology ; Materials Science, Multidisciplinary ; Metallurgy & Metallurgical Engineering
研究领域[WOS]	Science & Technology - Other Topics ; Materials Science ; Metallurgy & Metallurgical Engineering
关键词[WOS]	DIP-PEN NANOLITHOGRAPHY ; GEOMETRY OPTIMIZATION ; CRYSTAL-STRUCTURE ; QUANTUM ; NITRILOTRIACETATE ; PROTEINS ; PROGRAM ; MODELS ; IMOMM
收录类别	SCI
语种	英语
WOS记录号	WOS:000237817400017
公开日期	2007-06-15 ; 2007-12-05 ; 2009-06-23
内容类型	期刊论文
源URL	[http://dspace.imech.ac.cn/handle/311007/17181]
专题	力学研究所_力学所知识产出(1956-2008)
推荐引用方式 GB/T 7714	Yang ZY,Zhao YP. QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface[J]. Materials Science and Engineering A-Structural Materials Properties Microstructure and Processing,2006.
APA	杨振宇,&赵亚溥.(2006).QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface.Materials Science and Engineering A-Structural Materials Properties Microstructure and Processing.
MLA	杨振宇,et al."QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface".Materials Science and Engineering A-Structural Materials Properties Microstructure and Processing (2006).