3.8.4 Secondary structure changes during simulation
The average secondary structure transitions in each of the simulations were monitored using Define Secondary Structure of Proteins (DSSP) program 78. Simulations started from residues in contact with the interface (DNA); these residues include both the N- and C-termini of both the monomers of IRX4. A scan be seen in Fig S8 and S9, the N-terminal region of the homeodomain have attained quite a distinct secondary structure compare to the mutants. Secondary structure analysis was used to identify the extent of changes which helps in promoting the structural integrity of the binding. Compared to the native structure, A149V after initial 50 ns showed a robust helical propensity compared to other mutants. The helical conformation amongst the other mutants were consistently altered throughout the 200ns simulations involving turn structures. Interestingly the smallest helix consisting of 9 amino acid (174-182) didn’t show any major differences along the different mutants. Examination of individual residue energy difference highlights the fact there is reorientation of the protein from its initial orientation in the mutants, highlighting the effect of the variants on DNA binding. The final orientation and secondary structure in all the variants is different, exhibiting loss of loss or gain in bending of the helix.