3.8.3 Hydrogen bond analysis of protein-DNA complex
Hydrogen bonds were analyzed between the IRX4 homeodomain-DNA complex to find important residues involved in hydrogen bonding. The key criteria for this analysis were as previously reported77. A total of 7 hydrogen bonds were observed at the protein-DNA interface for the WT IRX4 protein as reported in Table 4. The hydrogen bonds are illustrated as donor-acceptor bonds between DNA and protein. The atoms represent the side chain and backbone of the DNA and protein. The residues K145, A149, Y169, S190, R197 and R199 were involved in forming multiple hydrogen bonds and stabilizing the interactions. Hydrogen bonds having fractions of more than 0.5 were considered as having interaction between DNA and amino acids. There was a loss of hydrogen bonds in the arginine mutant variants which highlighted the conservation of these residues in DNA recognition. There was loss of hydrogen bonds in all the mutants. Weak hydrogen bonds were formed between residues compared to WT protein which showed change in flexibility of the residues binding to DNA. The Arginines on the C-terminal side of the homedomain when mutated affected hydrogen bonding shown in Table 5. The N-terminal Arginines showed hydrogen compensation when mutated resulting in formation of weak hydrogen bonds to maintain the stability of protein-DNA complex.