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 central role in gene regulation. We use homeodomain as a model system to study the specific interactions between protein and DNA in a complex. Following the fundamental concept of homology modeling, we have developed an algorithm for predicting structures of both protein and DNA using the known structure of a similar complex as the template. The accuracies of the algorithm in predicting the complex structures are evaluated when two of the homeodomain protein-DNA complexes with known structures (antennapedia and MATalpha2) are selected as test systems. This algorithm allows structural studies of homeodomain binds to DNA with different sequences.
Tung
C S
CS
Theoretical Biology and Biophysics (T-10), Theoretical Division, Los Alamos National Laboratory, NM 87545, USA. cst@t10.lanl.gov
D000595:Amino Acid Sequence; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D005800:Genes, Fungal / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid
D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D004247:DNA