Remorin-AMOEBA

Depository gathering all the relevant data for the work published in the following Manuscript:Dynamic pre-structuration of lipid nanodomain-segregating remorin proteins(https://doi.org/10.21203/rs.3.rs-4364507/v1).

Folders without FF mention contain simulations performed with AMOEBA :This repository contains all molecular dynamics trajectories put to production regarding 13 Remorin systems, the associated pdb files, scripts used for visualisation and computing of observables.For practical reasons, the solvents molecules were removed from the simulations. The complete data including solvent are available upon request.

Below, a short description of the methodology :

All atom simulations using the polarizable force field AMOEBA (2018) in combination with the Tinker-HP Software (v1.3 2021).The systems underwent a minimization of 30 000 step using a L-BFGS optimizer. The next equilibration steps were realised using a timestep of 1fs, the RESPA integrator and the berendsen barostat (when relevant) unless stated otherwise. The solvent was then progressively heat up in the NVT ensemble, from 5K to 300K using 10K steps and spending 5ps at each temperature, before undergoing additional 100ps at 300K. The system was then allowed to slowly relax for 3 times 400ps in the NPT ensemble while applying harmonic restraints of 10, 5 and finally 1 kcal/mol/A on the backbone atoms of the protein. Then, all restraints were removed, and we used the montecarlo barostat in combination with the BAOAB-RESPA1 propagator. Three final equilibration steps were performed for 100ps, 200ps and 500 ps by respectively increasing the outer timestep from 1fs to 2fs, to 5fs up to 10fs.Regarding the production run, all calculations were performed in the NPT ensemble, using the montecarlo barostat and the BAOAB-RESPA1 propagator with an outer timestep of 10fs, and hydrogen mass repartioning. 1.04 µs long Adaptive sampling simulations were generated on thirteen small remorin systems and 560ns long simulation on 1 dimer system, resulting in a total of 14.08 µs.

Python files necessary to the reproduction of  figures are available in this repository. The definition of weights necessary to unbias simulations are available under the form of "debiasage.txt" files.Folders with "AMBER" mention contain simulations performed with AMBER99 or AMBER14SB:For practical reasons, the solvents molecules were removed from the simulations. The complete data including solvent are available upon request.All simulation using non-polarizable force fields were performed using the GROMACS 6 software, following a standard protocol to minimize, equilibrate, and execute the production run of the molecular system69. Energy minimisation was performed using the steepest descent algorithm for 50 000 steps. Subsequently, the equilibrations under NVT and NPT conditions were performed at 300K during 100 ps each, using a Van der Walls and Coulomb cutoff of 1.0 nm each. For equilibration and production runs, we used the velocity-rescaling thermostat, with a time constant of 0.1 ps, coupled separately for the protein and the solvent (ions and water) and the Parrinello-Rahman barostat (when relevant) with a time constant of 2.0 ps , a compressibility of 4.5 × 10-5 bar-1 and at a pressure of 1 bar. During the equilibration phase, the non-hydrogen protein atoms were restrained by a force constant of 1,000 kJ mol 1nm-2. Long-range electrostatics were modeled using the Particle-Mesh Ewald method. All bonds were treated using the LINCS algorithm. The integration time step was 2 fs for equilibration and production.Scripts to be used for the figures are the same than the ones used in AMOEBA simulations without using weights.