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

doi:10.1016/j.msea.2005.10.078

IMECH-IR > 力学所知识产出(1956-2008)

	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); Zhao, YP (reprint author), Chinese Acad Sci, Inst Mech, State Key Lab Nonlinear Mech, Beijing 100080, Peoples R China.
发表期刊	Materials Science and Engineering A-Structural Materials Properties Microstructure and Processing
	2006
ISSN	0921-5093
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.
学科领域	力学
DOI	10.1016/j.msea.2005.10.078
收录类别	SCI
语种	英语
WOS记录号	WOS:000237817400017
关键词[WOS]	DIP-PEN NANOLITHOGRAPHY ; GEOMETRY OPTIMIZATION ; CRYSTAL-STRUCTURE ; QUANTUM ; NITRILOTRIACETATE ; PROTEINS ; PROGRAM ; MODELS ; IMOMM
WOS研究方向	Science & Technology - Other Topics ; Materials Science ; Metallurgy & Metallurgical Engineering
WOS类目	Nanoscience & Nanotechnology ; Materials Science, Multidisciplinary ; Metallurgy & Metallurgical Engineering
引用统计	被引频次：12[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://dspace.imech.ac.cn/handle/311007/17181
专题	力学所知识产出(1956-2008)
通讯作者	Zhao, YP (reprint author), Chinese Acad Sci, Inst Mech, State Key Lab Nonlinear Mech, Beijing 100080, Peoples R China.
推荐引用方式 GB/T 7714	Yang ZY,Zhao YP,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,&Zhao, YP .(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).

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