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.