Structural study of homeodomain protein-DNA complexes using a homology modeling approach

The homeodomain is a conserved protein motif that binds to DNA and plays a centrol role in gene regulation. We use homeodomain as a model system to st udy the specific interactions between protein and DNA in a complex. Followi ng the fundamental concept of homology modeling, we have developed an algor ithm for predicting structures of both protein and DNA using the known stru cture of a similar complex as the template. The accuracies of the algorithm in predicting the complex structures are evaluated when two of the homeodo main protein-DNA complexes with known structures (antennapedia and MAT alph a R) are selected as test systems. This algorithm allows structural studies of homeodomain binds to DNA with different sequences.