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.