Fig. 5: Application of the pipeline to a range of example proteins.

The LipIDens pipeline applied to assist interpretation of lipid-like densities within structures of a–e the Erwinia pentameric ligand-gated ion channel (ELIC, PDBid 7L6Q)³⁷, f–i the proton channel Otopetrin1 (OTOP1, PDBid 6NF4)³⁶ and j, k the E. coli mechanosensitive ion channel (MscS, PDBid 7ONJ)³⁸. a Overlay of the structurally modelled cardiolipin (CDL) pose on ELIC (magenta) with the pose at the end (t = 200 ns) of an atomistic simulation (teal) initiated from the top ranked CG CDL binding pose. Phosphate groups of each CDL molecule are shown as spheres connected by a vector indicating the relative lipid tilt angle. b Angle of the vector with respect to z across n = 3 ×200 ns independent atomistic simulations (teal). The magenta line indicates the structurally modelled lipid tilt angle (153°). Box plot divisions for n = 3003 angles measured: lower quartile (82°), median (92°), upper quartile (103°), whiskers excluding outliers (minimum: 53°, maximum: 134°). c Discontinuity between the lipid-like densities within the upper (teal) and lower (dark teal) leaflets across the bilayer midplane. Relative residence times for PE, PG and CDL binding to the identified upper (d) and lower (e) sites (defined as in Fig. 4), across n = 10 ×15 μs independent CG simulations. Asymmetric residence time error bars report the second k_off value calculated via bootstrapping (also applies to parts g, h and j). f Lipid-like densities surrounding OTOP1 coloured according to whether bound cholesterol (green) or PIP₂/PS (red) were among the highest site residence times. Other lipid densities where sites were identified by PyLipID are shown in blue (see Supplementary Fig. 4) and densities where sites were not identified are dark blue. g Exclusive binding of cholesterol between the OTOP1 N- and C- domains, corresponding to the cholesterol site modelled in the structure³⁶. h Preferential binding of anionic lipids at a kinked lipid density at the OTOP1 dimer interface. i Top ranked PIP₂ binding pose identified by PyLipID from CG simulations, showing curved tail position which matches the lipid density at this site. j Prolonged interactions of PE, PG and CDL with MscS between TM2 and TM3a. k Comparison of the top ranked CDL binding pose from CG simulations (left) with the modelled PE and DDM molecules in the MscS structure (right) showing tail insertion/stacking between TM2 and TM3a and a tilted lipid binding pose.