3.9.1 Energy landscape changes in nucleotides
The simulated complex of the IRX4-DNA was subjected to energy calculation difference amongst the different nucleotide residues in the DNA (Figure 11). When compared to the native protein, all the variants showed a decrease in energy profiles amongst the nucleotide. This highlights the fact that there was a decrease in binding potential of the residues to DNA nucleotides. The maximum fluctuations were seen at the DNA binding residues pronouncing the role of these residues in binding. Consequently, all the variants were rigid in nature with changes in the amino acid sequence resulting in decrease in the interaction of the molecules. Importantly the residue R197, R198 and R199 showed the most fluctuations in the energy landscape of the DNA molecule, showing the importance of the C-terminal Arginines in stabilizing the DNA fluctuations. Previous results on arginine mutants in the DNA binding domain of STAT3 have shown changes in intracellular shuttling and phosphorylation79. This also confirms that point mutations at the DNA binding residues causes a destabilizing effect leading to protein compactness and change in binding potential. Additionally, these mutations can also generate neomorphic functions resulting in disease phenotype.