A homology-based molecular model of the proline-rich homeodomain protein Prh, from haematopoietic cells

A molecular structural model for the homeodomain of the haematopoietic protein Prh together with its DNA recognition sequence, has been built using the known crystal structure of the MAT alpha 2 homeodomain as a starting-point. The modelling procedure used main and side-chain optimisations by means of molecular mechanics/simulated annealing procedures to obtain stereochemically plausible geometries. The resulting structure has a number of specific interactions in both major and minor grooves of the DNA that serve to define the consensus binding sequence for Prh. In particular, the side-chain of glutamine 50 is postulated to be involved in hydrogen bonds to adjacent adenine and cytosine bases within the consensus sequence.