【作者】 贺仲金；

【导师】 周健； Ben Corry；

【作者基本信息】 华南理工大学 ， 化学工程， 2014， 博士

【摘要】 生物通道蛋白具有各种优异的性能和多种功能,如以非常高的通透性和选择性进行快速传质以及通水阻盐、极高的离子选择性、离子电流整流和感知环境变化实现智能门控响应等功能。基于分子动力学模拟,本研究通过模仿生物通道蛋白的关键结构和机制,将其优异性能和功能移植到仿生纳米通道；具有广泛的应用价值,如化工分离、纳米医药、用于海水脱盐淡化的高效反渗透膜和用于精确化学分析的新型纳流控系统；设计仿生纳米通道有助于阐明实现生物通道各种功能的必需因素,还可发现电解质溶液在纳米通道受限环境下的新现象和新规律,具有深远的理论意义。此外,本研究探索氨基酸用于碳纳米管水相分散。采用拉伸分子动力学模拟和伞形取样法研究Na+、K+和Cl-通过(6,6)、(7,7)、(8,8)、(9,9)和(10,10)椅型碳纳米管的过程,并分析离子在碳管中的水化行为。结果表明,离子通过管径较窄的碳管时,在入口处遇到较大的阻力,从出口进入本体相较容易；而通过管径相对较宽的碳管则几乎无阻碍。离子通过碳管的能垒随管径的增大而降低,不同离子的能垒各不相同,表明碳管具有固有的离子选择性；离子通过碳管时,不仅其配位数改变了,而且配位层中水分子的取向也有所改变,这两者共同决定了离子进入碳管时的去水化能,进而影响离子通过碳管的能垒和碳管的离子选择性。在(8,8)管中,Na+和K+与水分子的作用比在本体相中还要强,而在其他几个管中,要弱于或者类似于本体相。在本体相中,离子与水分子之间的静电作用使得水分子在离子周围呈现特定的取向,而当受限在碳纳米管中,Na+和K+第一配位层水分子之间形成的氢键显著地扰乱这一取向。但是,(8,8)管例外,水分子在此碳管中形成了一种类似于冰的独特结构,使水分子呈现特定的取向,这种水分子偶极取向对Na+和K+水化更加有利。与阳离子水化不同,在决定Cl-与水分子的作用大小方面,离子配位数比配位层中水分子的取向起更主导作用。此外,离子在管中特定的径向位置偏好对于离子水化也有一定影响。受生物离子通道蛋白关键结构的启发,本研究采用分子动力学模拟设计仿生石墨烯孔来区分非常相似性的Na+和K+结果发现,在跨膜电位差驱动下,用4个羰基修饰以模仿KcsA K+通道过滤器的石墨烯孔选择性地传输K+；而用4个羧基基修饰模仿NavAbNa+通道过滤器的石墨烯孔选择性地结合Na+,但选择性地传输K+。用3个羧基修饰孔径较窄的石墨烯孔,通过改变跨膜电位差的大小可调控其离子选择性：低电位差下,以单队列形式选择性传输Na+,“敲击”离子传输模式(knock-on)和石墨烯孔被Na+选择性阻塞这2个因素相结合得到Na+选择性；高电位差下,石墨烯被Na+阻塞这一构型变得不稳定,再加之羧基对Na+更强的亲和力使得Na+通过石墨烯的速度比K+更慢,从而得到K+选择性。许多生物通道的门控区域由疏水残基组成狭窄通道,能够阻碍离子传输,即便在物理意义上未完全关闭的状态下,受这一疏水门控机制的启发,我们采用分子动力学模拟设计了一个纳米门控装置,施加外力使(12,12)碳纳米管中部变形,形成一个狭窄区域以控制离子传输。施加电场驱动K+和Cl-在纳米管中流动。模拟结果显示增大外力使纳米管狭窄区域变窄从而降低管中的离子流量。当外力大于5nN时,狭窄区域使K+和Cl-部分去水化而彻底中断其传输,但仍能获得可观的水流量。当外力一旦撤走,离子传输可以恢复到未受扰动的水平,表明此门控装置能可逆地控制离子传输。这个外力可由现有的实验设备施加,如原子力显微镜的针尖。此外还发现在完全填充水分子的疏水狭窄区域内,离子部分去水化就能够关闭纳米通道,并不需要狭窄区域本身完全反润湿。采用分子动力学模拟研究在浓度为0.17M、pH7.0下,20种天然氨基酸在(6,6)碳纳米管表面吸附行为。结果表明,这20种氨基酸中,苯丙氨酸、酪氨酸、色氨酸和精氨酸表现出对碳管最强的亲和力,它们吸附到碳管表面并形成非常稳定的氨基酸聚集物。苯丙氨酸、酪氨酸和色氨酸通过侧链芳香环与碳管形成非常强的π-π堆积作用。精氨酸对碳管的强吸引作用主要归因于侧链胍基,它直接与碳管作用,并形成多个盐桥。这些吸附在碳管表面氨基酸的带负电的羧基和带正电的氨基指向水溶液,从而促进碳管在水中的分散,并可能通过静电排斥防止碳管凝聚。本研究为氨基酸用作新型的碳管分散剂提供理论支撑,并有助于理解碳管与蛋白质的作用。更多还原

【Abstract】 Biological protein channels have many remarkable properties and fascinating functions,such as fast mass-transport with high permeability and selectivity, high water permeabilitywith salt-rejection, ion-selectivity, gating, ionic current-rectification and environmentalresponsiveness. Using molecular dynamics (MD) simulations, this study aims to transplantthese properties and functions to biomimetic nanochannels by mimicking the key structuresand mechanisms of biological channel proteins, which might lead to a wide range of potentialapplications, such as in chemical separation, nanomedicines, reverse osmosis desalinationmembranes and novel nanofluidic systems for accurate chemical analysis. The successfuldesign of biomimetic nanochannels may help elucidate the essential ingredients for thefunctions of biological channels. This study could discover new phenomenon arising inelectrolyte solutions confined in nanochannels. Additionally, the suitability of amino acids forcarbon nanotube (CNT) aqueous dispersions is assessed in this study.Steered MD and umbrella sampling simulations are performed to study the process ofNa+, K+and Cl traversing through (6,6),(7,7),(8,8),(9,9) and (10,10) CNTs and ionhydration in CNTs is analyzed. The results show that ions are hindered from entering narrowCNTs at the entrance; however, it is easy for ions to leave narrow CNTs into bulk solution atthe exit. There is almost no hindrance for ions to translocate through wide CNTs. The freeenergy barriers for ions translocating through CNTs decrease sharply with the increase ofdiameter. Different free energy barriers of Na+, K+and Cl entering CNTs indicate that CNTshave an inherent ion selectivity. When ions traverse through CNTs, coordination numbers andpreferential orientation of water molecules in coordination shells of ions are different fromthose in bulk, which determine the dehydration energies of ions and affect free energy barriersof ions traversing CNTs and the ion selectivity of CNTs. It is found that the interaction of Na+and K+with the water molecules is enhanced in CNT(8,8), but is similar or weaker than inbulk in the other CNTs. In bulk, water molecules orient in specific directions around ions dueto the electrostatic interaction between them. Under the confinement of CNTs, the hydrogenbonds formed in the first hydration shell of Na+and K+disturb this orientation greatly. Anexception is in CNT(8,8), where the dipole orientation is even more favorable for cations thanin bulk due to the formation of a unique ice-like water structure that aligns the watermolecules in specific directions. In contrast, the coordination number is more important thanhydration shell orientation in determining the Cl--water interaction. Additionally, thepreference for ions to adopt specific radial positions in the CNTs also affects ionic hydration. Inspired by the key structures of biological ion channel proteins, we have performed MDsimulations to design biomimetic graphene nanopores that can discriminate between Na+andK+, two ions with very similar properties. The simulation results show that undertransmembrane voltage bias, a nanopore containing four carbonyl groups to mimic theselectivity filter of the KcsA K+channel, preferentially conducts K+over Na+. A nanoporefunctionalized by four negatively charged carboxylate groups to mimic the selectivity filter ofthe NavAb Na+channel, selectively binds Na+but transports K+over Na+. Interestingly, theion selectivity of the smaller diameter pore containing three carboxylate groups can be tunedby changing the magnitude of the applied voltage bias. Under lower voltage bias, it transportsions in a single file manner and exhibits Na+selectivity, dictated by the knock-on ionconduction and selective blockage by Na+. Under higher voltage bias, the nanopore is K+selective, as the blockage by Na+is destabilized and the stronger affinity for carboxylategroups slows the passage of Na+compared with K+.Gates in many biological channels are formed by a constriction ringed with hydrophobicresidues which can prevent ion conduction even when they are not completely physicallyoccluded. We use MD simulations to design a nanogate inspired by this hydrophobic gatingmechanism. Deforming a CNT(12,12) with an external force can form a hydrophobicconstriction in the tube centre that controls ion conduction. The simulation results show thatincreasing the magnitude of the applied force narrows the constriction and lowers the fluxesof K+and Cl-found under an electric field. With the exerted force lager than5nN, theconstriction blocks the conduction of K+and Cl-due to partial dehydration while allowing fora noticeable water flux. Ion conduction can revert back to the unperturbed level upon theforce retraction, suggesting the reversibility of the nanogate. The force can be exerted byavailable experimental facilities, such as atomic force microscope (AFM) tips. It is found thatpartial dehydration in a continuous water-filled hydrophobic constriction is enough to closethe channel, while full dewetting is not necessarily required.The adsorption of20standard amino acids on CNT(6,6) at a concentration of0.17M andpH7.0has been studied by MD simulations. Simulation results show that among the20amino acids, phenylalanine, tyrosine, tryptophan and arginine exhibit the strongest affinity forCNT(6,6). They adsorb to the tube and form very stable aggregates. Phenylalanine, tyrosineand tryptophan interact with the tube via the strong stacking of their aromatic rings.Interestingly, the strong attraction of arginine to CNT(6,6) mainly attributes to itsguanidinium group, which strongly interacts with the tube and forms multiple salt bridges.The negatively charged carboxylate and positively charged ammonium groups of these adsorbed amino acids extend away from the tube surface and point towards aqueous solution,which facilitates the solubilization of CNTs in water, and may be able to provide electrostaticrepulsion forces to prevent CNT agglomeration. The results of this work provide a theoreticalsupport for using amino acids as novel CNT dispersing agents and help to understandCNT-protein interactions.更多还原