4.4.2 MD simulation of docked complexes
MD simulation for 100 nanoseconds (ns) using Gromacs software 2020.5 was performed to evaluate the stability of docked complexes of whole Rv2615c protein with CARD-APAF1 and CARD-Caspase9 separately and mutant Rv2615c with CARD-APAF1 and CARD-Caspase9 separately. The docked structure of APAF1-CARD and Caspase9-CARD (PDB ID: 3YGS) was included as positive control in the simulation studies. The docked complex was solvated by TIP3P [transferable intermolecular potential with 3 points] water model using CHARMM36 force field. The final MD simulation run was performed at 300K temperature and standard pressure of 1.01 bar using NPT (number of particle [N], system pressure [P] and temperature [T]) and NVT (number of particle [N], system volume [V] and temperature [T]) ensemble. Backbone Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) of the entire complex was calculated and plotted.