2.1.4 Validation of docking results through MD simulation
The RMSD and RMSF plots obtained after the extensive (100 ns) MD
simulation confirmed the structural stability of the protein-protein
complexes (Fig 7). The RMSD value of backbone for all the complexes
increased for initial 10 to 20ns following which it became stable with
an average value of 1nm to 1.2nm for Rv2615c-APAF1 CARD and
Rv2615c-Caspase9 CARD till 100ns. The RMSD value for mutant
Rv2615c-APAF1 CARD was comparable to that of Rv2615c- APAF1 CARD while
the RMSD value of mutant Rv2615c-Caspase9 CARD was higher in the range
of 1.4nm. The average RMSD value of control structure was 0.70nm. RMSF
analysis revealed that the docked complexes of Rv2615c protein with
APAF1-CARD and Caspase9-CARD and mutant Rv2615c with Caspase9-CARD
displayed average RMSF value of 0.80nm. Mutant Rv2615c with APAF1-CARD
showed high fluctuations with average RMSF value in range of 1.20nm. The
average RMSF value of control structure was 0.30nm. Overall, MD
simulation results revealed that the docked complexes of Rv2615c showed
a comparatively higher RMSD and RMSF value than control structure
(APAF1-CARD with Caspase9-CARD) but all values are in acceptable range.
One reason for this higher RMSD and RMSF values of Rv2615c docked
structures could be large size of Rv2615c protein (461 residues) in
comparison to the APAF1-CARD (95 residues) and Caspase9-CARD structures
(97 residues).