Abstract
Models of the homodimer of HNF4alpha (Hepatocyte Nuclear Factor 4alpha) were built, based on the crystal structures of two domains, the DNA binding domain (DBD) and ligand binding domain (LBD) that form a significant portion of the complete structure (amino acids 49-369 of 455). Molecular dynamics simulations of the resultant models have revealed some interesting insights into a more complete structure than the separate crystal structures indicate. These are a novel area of dimerization between two monomers of a homodimer, novel interactions between monomers in previously investigated regions; that have the potential to be areas in which mutations may cause a disruption to the structure and/ or function of the homodimer. A potential explanation as to the repressive function of the repressor region found at the C-terminus of the sequence is also postulated. X-ray crystal structures of the antibiotic oligomycin (forms A, B and C) published by Palmer and Potter, 2008, were investigated to examine their binding to ATP Synthase. The x-ray crystal structure of the A form showed some anomalous features which were investigated with the aid of ab initio molecular orbital calculations. A model of the ATP Synthase Fo domain was modified by the addition of a missing segment of the stationary subunit a. The new model was used in a series of protein-ligand docking studies of the x-ray crystal structures of the antibiotic oligomycin, which were used as starting conformations for the docking studies. It was shown that oligomycin binds to the proton translocating residues of the ATP Synthase Fo domain, preventing both the passage of protons across the membrane and the rotation of the c-ring that results in the catalysis of ATP synthesis. It was shown that the forms of oligomycin that were the most effective inhibitors were the B and C forms, despite the natural abundance of the A form. Calculated binding constants for the bound conformations of all three forms correlate with the reported experimental values for a mix of all three forms.