Calculation of RMSF

RMSF was calculated as previously described [47,49,50] to quantify the structural dynamics of molecules in the MD simulations. The RMSF of Cα atoms was calculated to obtain information about atomic fluctuations of individual amino acid residues during the MD simulations. The 15,000 snapshots, obtained from MD simulations at 70–100 ns, were used to calculate the RMSF. The average structure obtained during 70–100 ns of MD simulation was used as the reference structure for RMSF calculation. RMSF, which quantifies differences between average values and those obtained at a given time of MD simulation, was calculated using the ptraj module in Amber, a trajectory analysis tool.