DOI: 10.5061/dryad.z8w9ghxk5
title: Molecular dynamics simulation data of ELIC in nanodiscs

description: 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.
description: 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.
description: # Molecular Dynamics Simulation Data of ELIC in Nanodiscs
 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 labeled as "Run N"
 where 'N' is the independent replicate number. Each run
 directory contains the starting structures (as a
 '.psf'/'.pdb' pair), configuration files
 ('.conf'), and a downsampled trajectory file ('.dcd').
 In each run directory, you will also find a file labeled
 'extraBonds.txt'. This is a NAMD extra bonds file to ensure that
 the included agonist, propylamine, remained in the binding pocket for the
 duration of the simulation. For completeness, the topology and parameter
 files for propylamine generated by the CGenFF server are also included as
 a top level file labeled "propylamine.str". These are provided
 as combined "stream" files (containing both the topology and
 parameters in a single file. Besides these parameters, the standard
 CHARMM36 force field parameters were used and are not included here.
 Lastly, there is a top level file labeled "scripts". This folder
 contains the scripts used for data analysis of the included trajectories.
 There are Tcl and Python scripts. The versions contained herein will not
 be updated and were the exact scripts used to analyze the data contained
 herein. See below for a link to a maintained version of these analysis
 scripts as well as a description of the scripts included. ##
 Sharing/Access information As stated above, the analysis scripts here will
 not be updated. There will be a maintained version of the analysis scripts
 at: ## Code/Software
 Within the "Scripts" directory, there are files used for
 analysis of the trajectory data. "NanodiscAnalysis.tcl" is the
 main analysis script used for this dataset. It relies on two outside
 scripts, namely "procedures.tcl" which contains some basic
 functions and "ellipse.py" which calculates the ellipse of best
 fit to measure nanodisc diameter. All functions within
 "nanodiscAnalysis.tcl" are documented as to what the input
 variables represent and the expected output. This information will not be
 repeated here. The analysis was performed using VMD (version 1.9.4a55)
 containing Tcl (version 8.5.6). The Python code was executed using version
 3.6.8.