2.6. Explicit solvent molecular dynamic (MD) simulations

The 5 lowest energy NMR structures of SRP1 were used as the initial coordinates to initiate five independent MD simulations. Each of the 5 replicas was solvated in a cubic TIP3P explicit solvent water-box with an average volume of ~55 × 55 × 55ų in CHARMM [24–26]. The system was then charge balanced with K⁺. Each of the solvated SRP1 structures was then energy minimized and equilibrated for 100 ps in the Charmm36 force field [27]. Five 600-ns production simulations at standard temperature and pressure were then performed using NAMD [28], together yielding a total of 3.0μs effective sampling of SRP1. Particle mesh Ewald was used for long-range electrostatic interactions and van der Waals interactions were smoothly switched off from 12 to 13Å [29]. Hydrogen mass was increased to 3 through bound heavy atom mass repartition [30]. The integration time-step was 4 fs, keeping all bonds to hydrogens atoms of fixed length with SHAKE [31]. Snapshots were saved at an interval of 10 ps for the duration of simulation time to be used for later analysis.