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., 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., , # Molecular Dynamics Simulation Data of ELIC in Nanodiscs

<https://doi.org/10.5061/dryad.z8w9ghxk5>

This data set is associated with Nature Communications (Manuscript Control Number: NCOMMS-22-45947). Contained here are three sets of molecular dynamics (MD) simulation trajectories described in the manuscript: ELIC wild-type in POPC planar bilayer, ELIC wild-type in a 9 nm nanodisc containing POPC, and ELIC wild-type in an 11 nm nanodisc containing POPC. In each simulation condition, three independent replicates were performed. The initial structures were generated with CHARMM-GUI. The MD data was generated using NAMD 2.14. Additional parameters for propylamine were generated with the CGenFF server and are provided here as well.

## Description of the data and file structure

At the top level, each simulation condition (i.e., planar bilayer, 9 nm nanodisc, and 11 nm nanodisc) have their own folder. Within each simulation condition, you will find each replicate has its own folder labele...,