3.8.2 Stability of IRX4 homeodomain-DNA complex
The protein-DNA complex was subjected to long MD simulations of 200ns
time period. We calculated root mean square fluctutation (RMSF) for
homeodomain-DNA complex. From the RMSF plot (Figure 8), it was observed
that the residues directly bound to DNA experienced slightly high
fluctuations in all the protein structures. The residues on the
C-terminal of the homeodomain were found to have slightly higher RMSF
values indicating flexibility of this region of the homedomain. The
residues 155-165 had lower RMSF values reflecting these residues to have
a good potential to be bound to DNA. Important residues, primarily the
one which were found to have binding to DNA showed less flexibility in
their conformational state. The mutants K172N and Y169F showed higher
fluctuations when the original amino acid were mutated compared to the
other mutants. Subsequent energy analysis of these residues and mutants
were done to confirm the effect of the mutations on binding to DNA.