Molecular dynamics simulation data of ELIC in nanodiscs

Lipid nanodiscs have become a standard tool for studying membrane proteins, including using single particle cryo-electron microscopy (cryo-EM). We find that reconstituting the pentameric ligand-gated ion channel (pLGIC), Erwinia ligand-gated ion channel (ELIC), in different nanodiscs produces distinct structures by cryo-EM. The effect of the nanodisc on ELIC structure extends to the extracellular domain and agonist binding site. Additionally, molecular dynamic simulations indicate that nanodiscs of different sizes impact ELIC structure and that the nanodisc scaffold directly interacts with ELIC. These findings suggest that the nanodisc plays a crucial role in determining the structure of pLGICs, and that reconstitution of ion channels in larger nanodiscs may better approximate a lipid membrane environment.

Methods
This data set represents all-atom molecular dynamics (MD) simulation of wild-type ELIC in a planar bilayer, a 9 nm nanodisc, and an 11 nm nanodisc (all containing POPC). These systems were constructed using the CHARMM-GUI web application. Simulations were performed using NAMD 2.14. The data has been downsampled at a ratio of 1:10 to be able to be made publicly available. In addition, some trajectories have had the periodic boundaries unwrapped to the central box. Otherwise, no post-processing has been done.

脂质纳米盘（Lipid nanodiscs）已成为研究膜蛋白的标准工具，相关应用亦涵盖单粒子冷冻电子显微镜（single particle cryo-electron microscopy, cryo-EM）领域。本研究发现，将五聚体配体门控离子通道（pentameric ligand-gated ion channel, pLGIC）——欧文氏菌配体门控离子通道（Erwinia ligand-gated ion channel, ELIC）——在不同纳米盘中重构后，通过冷冻电镜可观测到其结构存在显著差异。纳米盘对ELIC结构的影响可延伸至胞外结构域与激动剂结合位点。此外，分子动力学模拟结果表明，不同尺寸的纳米盘会对ELIC的结构产生影响，且纳米盘支架可直接与ELIC相互作用。上述研究结果提示，纳米盘在决定pLGIC的结构方面发挥着关键作用，而在更大尺寸的纳米盘中重构离子通道，或能更贴近真实的脂质膜环境。

方法
本数据集包含野生型ELIC分别在平面双分子层、9 nm纳米盘以及11 nm纳米盘（均含1-棕榈酰-2-油酰基-sn-甘油-3-磷酸胆碱，POPC）中开展的全原子分子动力学（all-atom molecular dynamics, MD）模拟数据。上述模拟体系均通过CHARMM-GUI在线应用程序构建，模拟计算采用NAMD 2.14完成。为实现公开共享，数据集已按1:10的比例进行降采样处理。此外，部分轨迹已解除周期性边界条件并中心化至模拟盒中。除此之外，未进行其他后处理操作。