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.