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.