3.3 Modelling of homeodomain using SWISS-MODEL
The three-dimensional structure of the homeodomain of human IRX4 is not
yet characterized using any biophysical methods like X-Ray or NMR.
Secondary structure prediction using PSIPRED was carried out on a
full-length sequence to check the ratio of secondary structures in the
sequence (Figure 4A). Homeodomain from residues 143-204 showed the
existence of 3 helices combined by the coiled region in between the
helices. The PSIPRED results matched with the modelling result from
SWISS-MODEL of the homeodomain, which correlated with the existence of 3
helices. The generated homology models were further subjected to an
overall model quality check. The models were subjected to backbone
dihedral angles (phi and psi) of the amino acid residues in the protein
structure. Ramachandran plot (Figure S5) generated by PROCHECK showed
98.2% of the residues in the most favoured regions, highlighting the
suitability and accuracy of the generated model67. The homology model
shared similar structural folds with the template, i.e., 4 α-helices, 3
helix-helix interactions, 2 β-turns, and 1 γ-turn ( Figure S6). We
further analyzed the conservation profile of individual amino acids in
the homeodomain structure. As expected, the most conserved amino acids
were exposed to the surface with direct contact with DNA (Figure 4B).
These residues were classified as conserved (N148, P168, W160, Y169,
P170, K175, Q188, W192, F193, N195, R197, R198, R199) and semi-conserved
(R146, K147, A149, L157, K172, A194). Apart from A194, all the other
residues were found to be exposed on the surface, potentially contacting
DNA, while all non-conserved residues are present on the distal surface.
Interestingly, there are no somatic mutations reported for this residue.