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Molecular dynamics simulations of carbon nanotube porins in lipid bilayers
Faraday Discussions ( IF 3.4 ) Pub Date : 2018-04-11 , DOI: 10.1039/c8fd00011e
Martin Vögele 1, 2, 3, 4 , Jürgen Köfinger 1, 2, 3, 4 , Gerhard Hummer 1, 2, 3, 4, 5
Affiliation  

Artificial channels made of carbon nanotube (CNT) porins are promising candidates for applications in filtration and molecular delivery devices. Their symmetric shape and high mechanical, chemical, and thermal stability ensure well-defined transport properties, and at the same time make them ideal model systems for more complicated membrane protein pores. As the technology to produce and tune CNTs advances, simulations can aid in the design of customized membrane porins. Here we concentrate on CNTs embedded in lipid membranes. To derive design guidelines, we systematically studied the interaction of CNT porins with their surrounding lipids. For our simulations, we developed an AMBER- and Lipid14-compatible parameterization scheme for CNTs with different chirality and with functional groups attached to their rim, and a flexible coarse-grained description for open-ended CNTs fitting to the MARTINI lipid model. We found that the interaction with lipid acyl chains is independent of the CNT chirality and the chemical details of functional groups at the CNT rims. The latter, however, are important for the interactions with lipid head groups, and for water permeability. The orientation and permeability of the pore are mainly determined by how well its hydrophobicity pattern matches the membrane. By identifying the factors that determine the structure both of isolated CNTs in lipid membranes and of CNT clusters, we set the foundation for a targeted design of CNT–membrane systems.

中文翻译:

脂质双层中碳纳米管孔的分子动力学模拟

由碳纳米管(CNT)孔制成的人工通道有望用于过滤和分子输送装置。它们的对称形状以及较高的机械,化学和热稳定性确保了明确的转运性质,同时使它们成为处理更复杂的膜蛋白孔的理想模型系统。随着生产和调节CNT的技术的发展,模拟可以帮助设计定制的膜孔。在这里,我们专注于脂质膜中嵌入的碳纳米管。为了得出设计准则,我们系统地研究了CNT孔蛋白与其周围脂质的相互作用。对于我们的仿真,我们为具有不同手性且官能团连接到其边缘的CNT开发了一种AMBER和Lipid14兼容的参数化方案,灵活的粗粒度描述,以适合于MARTINI脂质模型的开放式CNT。我们发现与脂酰基链的相互作用独立于CNT手性和CNT边缘官能团的化学细节。然而,后者对于与脂质头基的相互作用和透水性是重要的。孔的方向和渗透性主要取决于其疏水性与膜的匹配程度。通过确定决定脂膜中分离的CNTs结构和CNT簇结构的因素,我们为CNT-膜系统的目标设计奠定了基础。我们发现与脂酰基链的相互作用独立于CNT手性和CNT边缘官能团的化学细节。然而,后者对于与脂质头基的相互作用和透水性是重要的。孔的方向和渗透性主要取决于其疏水性与膜的匹配程度。通过确定决定脂膜中分离的CNTs结构和CNT簇结构的因素,我们为CNT-膜系统的目标设计奠定了基础。我们发现与脂酰基链的相互作用独立于CNT手性和CNT边缘官能团的化学细节。然而,后者对于与脂质头基的相互作用和透水性是重要的。孔的方向和渗透性主要取决于其疏水性与膜的匹配程度。通过确定决定脂膜中分离的CNTs结构和CNT簇结构的因素,我们为CNT-膜系统的目标设计奠定了基础。
更新日期:2018-09-28
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