蛋白质固液界面吸附的分子模拟
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摘要
蛋白质的界面吸附是一类基本的现象,也是解决界面科学、生命科学及工程技术领域中许多问题的关键,对蛋白质界面吸附问题的研究有着重要的理论和实际意义。由于蛋白质同界面间相互作用的复杂性使得单纯依靠实验方法无法得到吸附的完整信息。利用分子模拟方法,从微观水平上对蛋白质界面吸附进行研究,有助于深入地了解蛋白质界面吸附的机理。本论文采用CHARMM22力场和TIP3P水分子模型,在NVT条件下,对聚十赖氨酸分子在金属铂(Pt)、无机非金属氧化锌(ZnO)及有机高分子聚乙烯(PE)界面上的吸附过程分别进行了分子模拟(MD)。考察了不同界面性质、水溶液、力场参数等因素对吸附的影响。对聚十赖氨酸分子的构象变化、能量及运动等特性进行了分析,对蛋白质分子的固液界面吸附机理进行了探讨。
模拟结果表明,在不同性质的界面上,经过吸附后,聚十赖氨酸分子主链构象发生了变化,分子的α-螺旋结构有不同程度的减少。PE界面上的吸附作用强于Pt及ZnO界面,更易使聚十赖氨酸分子发生变性。在晶格结构界面上,界面原子排列密度越大对聚十赖氨酸分子的作用越强;界面原子排布规则的晶体界面对聚十赖氨酸分子构象的影响较无规则界面强。固体界面的组成性质及界面形态对蛋白质的吸附起到重要的影响作用。
对具有不同范德华参数和电荷的Pt界面上的聚十赖氨酸吸附体系进行的MD计算表明,范德华作用和静电作用在吸附中均对聚十赖氨酸分子构象产生影响,相对而言,静电力的作用影响更为显著,在吸附过程中起主导作用。
吸附过程中,水溶液在界面和聚十赖氨酸分子之间起到了重要的过渡媒介作用,聚十赖氨酸同界面的相互作用是聚十赖氨酸分子、固体界面及水溶液之间共同相互作用的结果,因此,界面的亲疏水性在蛋白质吸附中起着非常重要的作用。
采用分子模拟方法获得的结果,可以为蛋白质界面吸附的机理研究提供理论基础,对相关领域技术的发展起到促进作用。
Protein adsorption on interface is a common phenomena and a key to settle problems of surface science、biological science and engineering systems which is of great fundamental and practical importance. The complexity interaction between protein and surface make it impossible to get complete adsorption information only using experiment method. It is helpful to grasp protein adsorption mechanism using molecular simulation at the molecular level research. In this work, we focus on poly-ten-lysine interactions with several interfaces by MD techniques in which protein is modeled with the CHARMM22 parameter set, water molecules are described by the transferable intermolecular potentials with three-site point charge model (TIP3P), under NVT condition and the surfaces were platinum (Pt), znic oxide (ZnO) and polyethylene (PE). The influences of properties studied include the interface properties (interface structural and electrostriction nature), dynamic behavior of aqueous and different force field factors’influence during adsorption. Analyze the conformation, energy and motion of poly-ten-lysine. Discuss the mechanisms of poly-ten-lysine adsorption on solid-liquid interface.
Results reveal the interaction between poly-ten-lysine and interfaces make theα-helix conformation of poly-ten-lysine decrease to different extent. More distinct decrease even denatured happened on PE interfaces than Pt and ZnO interfaces. Besides, interface structural has important influence on adsorption. On different crytral lattic Pt interfaces, the more impact arrangement it is, the more stronger interaction between interface and poly-ten-lysine. The interaction between the protein and crystal interface is stronger than amorphous interface.
MD simulations on interfaces with different van der Waals parameters and charge show that interface interaction is to be dominated by electrostatic force interactions and van der Waals relatively weaker though they all affected adsorption conformation of poly-ten-lysine.
The interaction between the poly-ten-lysine and ZnO interface is mediated by aqueous. Interface interaction is the result of mutual interaction of the constituent elements of system, poly-ten-lysine, water and interface. Accordingly, hydrophobic nature of interface play an important role during adsorption, hydrophobic PE interfaces have stronger affection on protein conformation than hydrophilic interface.
Moreover, energy compositions and atom parameter of force field play an important role in simulation.
The molecular simulating results could offer theoretical basic for protein adsorption on interface and promote the development of related technology.
To better analyze results, another force field is used to the same interface condition which indicate that atom parameters of force field and energy items are the important factors that influence the simulation.
模拟结果表明,在不同性质的界面上,经过吸附后,聚十赖氨酸分子主链构象发生了变化,分子的α-螺旋结构有不同程度的减少。PE界面上的吸附作用强于Pt及ZnO界面,更易使聚十赖氨酸分子发生变性。在晶格结构界面上,界面原子排列密度越大对聚十赖氨酸分子的作用越强;界面原子排布规则的晶体界面对聚十赖氨酸分子构象的影响较无规则界面强。固体界面的组成性质及界面形态对蛋白质的吸附起到重要的影响作用。
对具有不同范德华参数和电荷的Pt界面上的聚十赖氨酸吸附体系进行的MD计算表明,范德华作用和静电作用在吸附中均对聚十赖氨酸分子构象产生影响,相对而言,静电力的作用影响更为显著,在吸附过程中起主导作用。
吸附过程中,水溶液在界面和聚十赖氨酸分子之间起到了重要的过渡媒介作用,聚十赖氨酸同界面的相互作用是聚十赖氨酸分子、固体界面及水溶液之间共同相互作用的结果,因此,界面的亲疏水性在蛋白质吸附中起着非常重要的作用。
采用分子模拟方法获得的结果,可以为蛋白质界面吸附的机理研究提供理论基础,对相关领域技术的发展起到促进作用。
Protein adsorption on interface is a common phenomena and a key to settle problems of surface science、biological science and engineering systems which is of great fundamental and practical importance. The complexity interaction between protein and surface make it impossible to get complete adsorption information only using experiment method. It is helpful to grasp protein adsorption mechanism using molecular simulation at the molecular level research. In this work, we focus on poly-ten-lysine interactions with several interfaces by MD techniques in which protein is modeled with the CHARMM22 parameter set, water molecules are described by the transferable intermolecular potentials with three-site point charge model (TIP3P), under NVT condition and the surfaces were platinum (Pt), znic oxide (ZnO) and polyethylene (PE). The influences of properties studied include the interface properties (interface structural and electrostriction nature), dynamic behavior of aqueous and different force field factors’influence during adsorption. Analyze the conformation, energy and motion of poly-ten-lysine. Discuss the mechanisms of poly-ten-lysine adsorption on solid-liquid interface.
Results reveal the interaction between poly-ten-lysine and interfaces make theα-helix conformation of poly-ten-lysine decrease to different extent. More distinct decrease even denatured happened on PE interfaces than Pt and ZnO interfaces. Besides, interface structural has important influence on adsorption. On different crytral lattic Pt interfaces, the more impact arrangement it is, the more stronger interaction between interface and poly-ten-lysine. The interaction between the protein and crystal interface is stronger than amorphous interface.
MD simulations on interfaces with different van der Waals parameters and charge show that interface interaction is to be dominated by electrostatic force interactions and van der Waals relatively weaker though they all affected adsorption conformation of poly-ten-lysine.
The interaction between the poly-ten-lysine and ZnO interface is mediated by aqueous. Interface interaction is the result of mutual interaction of the constituent elements of system, poly-ten-lysine, water and interface. Accordingly, hydrophobic nature of interface play an important role during adsorption, hydrophobic PE interfaces have stronger affection on protein conformation than hydrophilic interface.
Moreover, energy compositions and atom parameter of force field play an important role in simulation.
The molecular simulating results could offer theoretical basic for protein adsorption on interface and promote the development of related technology.
To better analyze results, another force field is used to the same interface condition which indicate that atom parameters of force field and energy items are the important factors that influence the simulation.
引文
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[3] 阎隆飞,孙之荣,蛋白质分子结构,北京:清华出版社,1999
[4] 沈同,王镜岩,生物化学 (上) 第二版,北京:高等教育出版社,1990
[5] 陶慰孙,李惟,姜涌明,蛋白质分子基础(第二版) ,北京:高等教育出版社,1995
[6] 耿信笃,白泉,王超展,蛋白质折叠液相色谱法,北京:科学出版社,2006
[7] 赵振国,吸附作用原理,北京:化学工业出版社,2006
[8] Nakanishi K, Sakiyama T, Imamura K. On the adsorption of proteins on solid surfaces, a common but very complicated phenomenon, Journal of Bioscience and Bioengineering, 2001, 91(3): 233–244
[9] He L, Dexter A F, Middelberg A P J. Biomolecular engineering at interfaces, Chemical Engineering Science, 2006, 61(3): 989–1003
[10] Gray J J, The interaction of proteins with solid surfaces, Current Opinion in Structural Biology, 2004, 14(1): 110–115
[11] 张辉,钟博,邓玉福,生命单元表面行为的物理表征,北京:科学出版社,2006
[12] 司士辉,生物传感器,北京:化学工业出版社,2002
[13] S L Burkett, M J Read. Adsorption-induced conformational changes of α-Helical peptides, Langmuir, 2001, 17: 5059–5065
[14] Simon O, Lumsdon, John Green, et al. Adsorption of hydrophobin proteins at hydrophobic and hydrophilic interfaces, Langmuir, 2005, 21: 8385–8388
[15] 陈百万,生物医学工程学,北京:科学出版社,1997
[16] 耿信笃,计量置换理论及应用,北京:科学出版社,2004,25
[17] 贺小贤,现代生物工程技术导论,北京:科学出版社,2005,303–305
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