Fig. 5: Quantifying the effects of the nanodisc environment.
From: Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel
Total (a) and hydrophobic (b) bilayer thickness are displayed relative to distance from the ELIC TMD surface for the 9 nm nanodisc (blue), 11 nm nanodisc (red), and planar bilayer (green) simulations. Data is presented as average across three independent simulations ( ± SD). The probability of ELIC contacting the MSP is shown for spMSP1D1ELIC in the 9 nm nanodisc (c) and 11 nm nanodisc (d). The probability was calculated over the last 250 ns of the simulation with a contact denoted by any atom of a given ELIC residue within 4.5 Å of any atom in the MSP. Residues with low contact probability are shown in blue and high contact probability in red. Residues with >25% contact probability are explicitly shown as licorice representations. Most residues with high contact probability are in M4. For each residue with a contact probability >25%, the ratio of interacting residue types from the scaffold protein is shown for the 9 nm (e) and 11 nm (f) nanodisc simulations.
