3.5 MD simulations of the WT protein-DNA complex
The protein-DNA system was subjected to 200 ns long MD simulations to
examine the stability and interactions within the complex. The WT
protein-DNA complex attained showed strong interactions with DNA at both
N- and C-terminal of the homeodomain. Additional interactions of
residues G143, T144, N148 and S190 were observed resulting in a more
compact and stable protein-DNA complex (Figure 6). The interactions from
the pre-MD model represents a snapshot from the MD-simulations after the
minimisation step whereas the post-MD model snapshots represents an
image of the interactions after 200ns. When comparing it to the template
6FQP, a vast array of amino acids have been found to be interacting on
the both chains of the protein to DNA. This highlights the importance of
strong and stable molecular interactions arginine, asparagine, threonine
and alanine in stabilizing the IRX4 protein-DNA complex.