Molecular dynamics simulations

All MD simulations were performed using GROMACS v5.1.2 ³⁹. The MemProtMD pipeline ⁴⁰ was used with the Martini 2.2 force field ⁴¹ to run five repeats of a 1 μs Coarse Grained (CG) MD simulation of the dimeric protein complexes. Last 800ns of each of these simulation trajectories were considered for further analysis. The proteins were centered within the simulation system to permit the assembly and equilibration of 10 % cardiolipin with either a 20% 1-palmitoly, 2-oleoyl, phosphatidylglycerol (POPG): 70% 1-palmitoyl, 2-oleoyl, phosphatidylethanolamine (POPE) or 90 % 1-palmitoyl, 2-oleoyl, phosphatidylcholine (POPC) bilayers. Systems were neutralised with a 150 mM concentration of NaCl. All simulations were performed at 323K, with protein, lipids and solvent separately coupled to an external bath using the velocity-rescale thermostat ⁴². Pressure was maintained at 1 bar with a semi-isotropic compressibility of 5 x 10^-6 using the Berendsen barostat ⁴³. All bonds were constrained with the P-LINCS algorithm ⁴⁴. Electrostatics was measured using the Reaction Field method ⁴⁵, while a Verlet cut-off scheme to permit GPU calculation of non-bonded contacts was used for Lennard-Jones parameters ⁴⁶. Simulations were performed with an integration time-step of 20 fs. Atomistic snapshots at the end-point of the CGMD simulations were created by using CG2AT ⁴⁷ in combination with Alchembed ⁴⁸. The lipid densities and contacts with the protein during the MD simulations were calculated using MDAnalysis ⁴⁹, and locally written code. All images and animations were generated using Pymol ⁵⁰.