Coarse-Grained Molecular Dynamics Simulations of SARS-CoV-2 E Protein embedded in 100% POPC membrane

Coarse-grained MD simulations of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in 100% POPC lipids. Unless otherwise noted, all simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps. Comparisons of different combinations of restraint scheme and run-time parameters took place in a 100% POPC membrane with E protein embedded. In two simulations, protein back-bone beads were restrained to their initial coordinates via harmonic potential with a force constant of 2,000 kJ mol−1 nm−1. We describe this style of restraint as “absolute position restraints". We performed two different simulations: one with run-time parameter refcoord_scaling set to all, and one with the setting turned off (refcoord_scaling no). Both simulations were then simulated in the NPT ensemble. The refcoord_scaling no simulation used GROMACS version 2021.6 and the v-rescale thermostat, but all other settings remained the same. We also performed two simulations with elastic network restraints instead of absolute position restraints. In our elastic networks, all protein backbone bead pairs within 1.4 nm of one another were bonded together with force constants of 5,000 kJ mol−1 nm−1 using the Martinize tool. One of these simulations (NPT ensemble) had identical settings to those listed in Common Settings. The second elastic network simulation (NVT ensemble) used GROMACS version 2021.6, the v-rescale thermostat, and utilized restraints to prevent diffusion, rotation, and tilt of the protein. Restraints were parameterized using the Colvars Dashboard. The absolute position restraint simulation with refcoord_scaling all ran for over 50 μs, with the membrane adopting a metastable conformation before 10 μs. The absolute position restraint simulation with refcoord_scaling no and the NPT elastic network simulation ran for at least 10 μs, which was more than sufficient for area per lipid (Σ) to converge. The NVT elastic network simulation ran for 2 μs.