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

AbstractA 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 MATα2 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