分子动力学
纳米孔
化学物理
离子键合
电场
离子
极化率
脂质双层
化学
离子液体
材料科学
纳米技术
膜
计算化学
分子
物理
有机化学
量子力学
生物化学
催化作用
作者
Delphine Dessaux,Jérôme Mathé,Rosa Ramirez,Nathalie Basdevant
标识
DOI:10.1021/acs.jpcb.2c01028
摘要
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since they allow longer and faster simulations. We performed coarse-grained molecular dynamics of the ionic transport through the α-hemolysin protein nanopore, inserted into a lipid bilayer surrounded by solvent and ions. For this purpose, we used the MARTINI coarse-grained force field and its polarizable water solvent (PW). Moreover, the electric potential difference applied experimentally was mimicked by the application of an electric field to the system. We present, in this study, the results of 1.5 μs long-molecular dynamics simulations of 12 different systems for which different charged amino acids were neutralized, each of them in the presence of nine different electric fields ranging between ±0.04 V/nm (a total of around 100 simulations). We were able to observe several specific features of this pore, current asymmetry and anion selectivity, in agreement with previous studies and experiments, and we identified the charged amino acids responsible for these current behaviors, therefore validating our coarse-grain approach to study ionic transport through nanopores. We also propose a microscopic explanation of these ionic current features using ionic density maps.
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