生物膜的结构与性质关系的模拟研究
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摘要
生物膜作为细胞的重要组成部分,它的结构与性质的关系对细胞生物学的发展和完善具有重要的意义。本文简要概述了生物膜的组成,结构和功能。介绍了生物膜的结构功能以及膜中磷脂分子和膜蛋白质分子性质的研究现状。由于目前对生物膜各方面性质的研究还存在不足,因此还需要进一步深入的研究。本文应用耗散粒子动力学方法(dissipative particle dynamics, DPD),在分子层面上对生物膜体系的动力学性质和微观状态进行了研究,取得了一些成果。
本文应用耗散粒子动力学方法(DPD)研究了在水溶液中表面活性剂包裹油性溶质形成的胶束与生物膜发生碰撞融合与溶质传递的过程。揭示了在此过程中,溶质如何通过胶束与生物膜的碰撞融合来进行物质传递,以及有哪些因素会影响整个过程。模拟结果表明胶束首先在水中与生物膜进行间歇性碰撞,然后胶束与生物膜发生融合,最后胶束中的溶质分子向生物膜进行传递与扩散。其中融合过程可以分为三个单元过程：(1)分子接触。(2)孔道形成。(3)孔道增长。在整个碰撞融合与溶质传递过程中,存在两个速度控制步骤,即胶束与生物膜间水膜的破裂和融合时孔道的产生。胶束的初始碰撞速度,表面张力,胶束与生物膜间亲水粒子间的相互作用力以及空间排斥等影响因素在模拟中被检测。结果发现在碰撞融合过程中,耗散力(depletion force)发挥了重要的作用。而胶束的初始碰撞速度对融合比率(fusion ratio)基本没有影响。胶束表面张力增强有助于孔道的生成,提高了融合比率。而胶束与生物膜间亲水粒子间的相互作用力以及空间排斥加大,则增加了融合时的能量壁垒,降低了融合比率。
由哑铃状双头磷脂分子(bolaform phospholipid)构成的古生菌细胞膜具有优良的热稳定性。例如耐热嗜酸古生菌(Sulfolobus acidocaldarius),能够在65-80℃的热温泉和酸性条件下(pH=2-3)生存。此种优良的热稳定性的原理还没有完全发现。本文应用耗散粒子动力学方法(DPD)使用囊泡结构作为模型研究了古生菌细胞膜在高温下的热稳定性和破裂机理。与由单极性磷脂分子(monopolar phospholipid)构成的普通细胞膜比较,发现了古生菌细胞膜结构与性质的关系。在分子层面,解释了古生菌细胞膜具有优良热稳定性的原因和破裂机理。
根据小电导率机械敏感性离子通道蛋白质(mechanosensitive ion channel of small conductance MscS)的结构与性质,本文建立了新的离子通道蛋白质粗粒化模型。在粗粒化过程中,离子通道蛋白质(MscS)的基本结构被保留。在耗散粒子动力学(DPD)模拟中发现,离子通道蛋白质模型根据模型参数的不同,存在两种不同的构型状态：打开状态和闭合状态。在膜表面张力相同条件下,离子通道的构型状态取决于蛋白质的结构,主要是蛋白质中的穿膜α螺旋的长度。模拟结果发现一定尺寸的蛋白质开关状态转变依靠膜表面张力的变化,性质和真实的小电导率机械敏感性离子通道蛋白质相同。
应用耗散粒子动力学(DPD)方法本文还研究了锚定蛋白质(anchored protein)在细胞膜上的自聚过程。模拟发现锚定蛋白质的聚集速度和程度与细胞膜中锚定蛋白质的疏水长度有关。锚定蛋白质的聚集机理是：蛋白质的插入使周围细胞膜的上下两层结构发生不同变化,并且上下两层彼此耦合,这种变化促使蛋白质发生聚集。只有当锚定蛋白质的渗透深度(penetration depth)超过半膜厚度,下层的细胞膜结构才会发生剧烈形变。插入细胞膜深度较浅的锚定蛋白质,周围的细胞膜厚度变化较小。而插入细胞膜较深的锚定蛋白质则使细胞膜厚度波动加大。本文将锚定蛋白质的聚集机理与穿膜蛋白质的聚集机理相比较,找出了它们的异同点。
The relationship of the structures and properties of biomembrane, which is an important component of cell, is very important for development and improvement of cell biology. It is introduced the component, structure, and function of biomembrane. And, the research of the structure and function of bilayer and properties of phospholipids and proteins of membrane, which have been studied by many scientists, are also presented in the paper. It is needed to develop deeply due to the lack of work of biomembrane. By using the dissipative particle dynamics method, the dynamical property and microstructure are studied in molecular details and some results are found.
The kinetic process of collision-driven solute transfer in an aqueous phase in which micelles are used as solute carriers is investigated by dissipative particle dynamics simulations. It is showed that in the transfer process of hydrophobic solute molecules, how the solute molecules are transferred through collision and fusion between micelle and bilayer and what factors affect the whole process. The simulation results indicate that, after a stage of intermittent collision between two neighboring aggregates, the fusion happens and the solute molecules transfer from the micelle to bilayer and diffuse. There are roughly three sequential events in a coalescence stage:(1) molecular contact, (2) neck formation, and (3) neck growth. It is found that there are two rate-limiting steps in the whole process of solute transfer, i.e., the break of the water film between two neighboring aggregates and the nucleation of a pore between two surfactant films. The effects of the collision velocity, the surface tension, the repulsive interaction between the surfactant films of the colliding aggregates, as well as the steric repulsion are examined. The simulation results show that the depletion force plays an important role during the coalescence stage, while the initial collision velocity basically does not change the fusion ratio. The results also demonstrate that the stronger of the surface tension facilitates the formation of the pores and increase of the fusion ratio. The effect of interaction between the colliding aggregates and the steric repulsion change the energy barrier and the fusion ratio.
It is known that the archaebacterial cell membrane, which is formed by the bolaform phospholipids, is thermal stability at high temperature. For example, the thermoacidophilic archaebacterium Sulfolobus acidocaldarius can grow in hot springs at 65-80℃and live in acidic environments (pH 2-3). However, the origin of its unusual thermal stability remains unclear. In this work, using a vesicle as a model, the thermal stability and rupture of archaebacterial cell membrane are studied by using dissipative particle dynamics method. The structure-property relationship of monolayer membrane formed by bolaform lipids is found by comparing it with that of bilayer membrane formed by monopolar lipids. The origin of the unusually thermal stability of archaebacterial cell and the mechanism for its rupture are presented in molecular details.
According to the structure and property of a kind of membrane protein, the mechanosensitive channel of small conductance (MscS), a coarse-grained model is proposed. The basic structure of the MscS is preserved when the protein is coarse grained. For the coarse-grained model, the channels show two different states, namely the open and closed states, depending on the model parameters in the dissipative particle dynamics simulations. Under the same membrane tension, the state of the ion channel is found to be critically determined by the protein structure, especially the length of three transmembrane a-helices. It is also found that for the protein with certain size, the gating transition occurs when the membrane tension is applied, resembling in a real mechanosensitive channel.
The cluster formation of anchored proteins in a membrane has been studied in this work by dissipative particle dynamics simulation. The rate and extent of clustering is found to be dependent on the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work is ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrate that only when the hydrophobic depth of anchored proteins is larger than half the membrane thickness, the structure of the lower monolayer can be significantly deformed. Moreover, studies on the local structures of membranes indicate weak perturbation of bilayer thickness for a shallowly inserted protein, whereas there is significant perturbation for a more deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.
本文应用耗散粒子动力学方法(DPD)研究了在水溶液中表面活性剂包裹油性溶质形成的胶束与生物膜发生碰撞融合与溶质传递的过程。揭示了在此过程中,溶质如何通过胶束与生物膜的碰撞融合来进行物质传递,以及有哪些因素会影响整个过程。模拟结果表明胶束首先在水中与生物膜进行间歇性碰撞,然后胶束与生物膜发生融合,最后胶束中的溶质分子向生物膜进行传递与扩散。其中融合过程可以分为三个单元过程：(1)分子接触。(2)孔道形成。(3)孔道增长。在整个碰撞融合与溶质传递过程中,存在两个速度控制步骤,即胶束与生物膜间水膜的破裂和融合时孔道的产生。胶束的初始碰撞速度,表面张力,胶束与生物膜间亲水粒子间的相互作用力以及空间排斥等影响因素在模拟中被检测。结果发现在碰撞融合过程中,耗散力(depletion force)发挥了重要的作用。而胶束的初始碰撞速度对融合比率(fusion ratio)基本没有影响。胶束表面张力增强有助于孔道的生成,提高了融合比率。而胶束与生物膜间亲水粒子间的相互作用力以及空间排斥加大,则增加了融合时的能量壁垒,降低了融合比率。
由哑铃状双头磷脂分子(bolaform phospholipid)构成的古生菌细胞膜具有优良的热稳定性。例如耐热嗜酸古生菌(Sulfolobus acidocaldarius),能够在65-80℃的热温泉和酸性条件下(pH=2-3)生存。此种优良的热稳定性的原理还没有完全发现。本文应用耗散粒子动力学方法(DPD)使用囊泡结构作为模型研究了古生菌细胞膜在高温下的热稳定性和破裂机理。与由单极性磷脂分子(monopolar phospholipid)构成的普通细胞膜比较,发现了古生菌细胞膜结构与性质的关系。在分子层面,解释了古生菌细胞膜具有优良热稳定性的原因和破裂机理。
根据小电导率机械敏感性离子通道蛋白质(mechanosensitive ion channel of small conductance MscS)的结构与性质,本文建立了新的离子通道蛋白质粗粒化模型。在粗粒化过程中,离子通道蛋白质(MscS)的基本结构被保留。在耗散粒子动力学(DPD)模拟中发现,离子通道蛋白质模型根据模型参数的不同,存在两种不同的构型状态：打开状态和闭合状态。在膜表面张力相同条件下,离子通道的构型状态取决于蛋白质的结构,主要是蛋白质中的穿膜α螺旋的长度。模拟结果发现一定尺寸的蛋白质开关状态转变依靠膜表面张力的变化,性质和真实的小电导率机械敏感性离子通道蛋白质相同。
应用耗散粒子动力学(DPD)方法本文还研究了锚定蛋白质(anchored protein)在细胞膜上的自聚过程。模拟发现锚定蛋白质的聚集速度和程度与细胞膜中锚定蛋白质的疏水长度有关。锚定蛋白质的聚集机理是：蛋白质的插入使周围细胞膜的上下两层结构发生不同变化,并且上下两层彼此耦合,这种变化促使蛋白质发生聚集。只有当锚定蛋白质的渗透深度(penetration depth)超过半膜厚度,下层的细胞膜结构才会发生剧烈形变。插入细胞膜深度较浅的锚定蛋白质,周围的细胞膜厚度变化较小。而插入细胞膜较深的锚定蛋白质则使细胞膜厚度波动加大。本文将锚定蛋白质的聚集机理与穿膜蛋白质的聚集机理相比较,找出了它们的异同点。
The relationship of the structures and properties of biomembrane, which is an important component of cell, is very important for development and improvement of cell biology. It is introduced the component, structure, and function of biomembrane. And, the research of the structure and function of bilayer and properties of phospholipids and proteins of membrane, which have been studied by many scientists, are also presented in the paper. It is needed to develop deeply due to the lack of work of biomembrane. By using the dissipative particle dynamics method, the dynamical property and microstructure are studied in molecular details and some results are found.
The kinetic process of collision-driven solute transfer in an aqueous phase in which micelles are used as solute carriers is investigated by dissipative particle dynamics simulations. It is showed that in the transfer process of hydrophobic solute molecules, how the solute molecules are transferred through collision and fusion between micelle and bilayer and what factors affect the whole process. The simulation results indicate that, after a stage of intermittent collision between two neighboring aggregates, the fusion happens and the solute molecules transfer from the micelle to bilayer and diffuse. There are roughly three sequential events in a coalescence stage:(1) molecular contact, (2) neck formation, and (3) neck growth. It is found that there are two rate-limiting steps in the whole process of solute transfer, i.e., the break of the water film between two neighboring aggregates and the nucleation of a pore between two surfactant films. The effects of the collision velocity, the surface tension, the repulsive interaction between the surfactant films of the colliding aggregates, as well as the steric repulsion are examined. The simulation results show that the depletion force plays an important role during the coalescence stage, while the initial collision velocity basically does not change the fusion ratio. The results also demonstrate that the stronger of the surface tension facilitates the formation of the pores and increase of the fusion ratio. The effect of interaction between the colliding aggregates and the steric repulsion change the energy barrier and the fusion ratio.
It is known that the archaebacterial cell membrane, which is formed by the bolaform phospholipids, is thermal stability at high temperature. For example, the thermoacidophilic archaebacterium Sulfolobus acidocaldarius can grow in hot springs at 65-80℃and live in acidic environments (pH 2-3). However, the origin of its unusual thermal stability remains unclear. In this work, using a vesicle as a model, the thermal stability and rupture of archaebacterial cell membrane are studied by using dissipative particle dynamics method. The structure-property relationship of monolayer membrane formed by bolaform lipids is found by comparing it with that of bilayer membrane formed by monopolar lipids. The origin of the unusually thermal stability of archaebacterial cell and the mechanism for its rupture are presented in molecular details.
According to the structure and property of a kind of membrane protein, the mechanosensitive channel of small conductance (MscS), a coarse-grained model is proposed. The basic structure of the MscS is preserved when the protein is coarse grained. For the coarse-grained model, the channels show two different states, namely the open and closed states, depending on the model parameters in the dissipative particle dynamics simulations. Under the same membrane tension, the state of the ion channel is found to be critically determined by the protein structure, especially the length of three transmembrane a-helices. It is also found that for the protein with certain size, the gating transition occurs when the membrane tension is applied, resembling in a real mechanosensitive channel.
The cluster formation of anchored proteins in a membrane has been studied in this work by dissipative particle dynamics simulation. The rate and extent of clustering is found to be dependent on the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work is ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrate that only when the hydrophobic depth of anchored proteins is larger than half the membrane thickness, the structure of the lower monolayer can be significantly deformed. Moreover, studies on the local structures of membranes indicate weak perturbation of bilayer thickness for a shallowly inserted protein, whereas there is significant perturbation for a more deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.
引文
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