MODELING THE STRUCTURE OF NAD BOUND TO PERTUSSIS TOXIN. Maxwell D. Cummings, Trevor N. Hart, Bart Hazes, and Randy J. Read. Departments of Biochemistry, and Medical Microbiology & Immunology, Universtiy of Alberta, Edmonton, AB, Canada, T6G 2H7. Ph:403-492-4696, Fax:403-492- 7521, Email: max@clouseau.mmid.ualberta.ca.

We describe a novel application of the technique known as fragment-based ligand design. This method is usually applied to the prediction of novel ligands for target binding sites. Libraries of molecular fragments are docked to the binding site(s) of interest; subsequently, collections of the dockings are connected to create novel potential ligands. We have used several new flexible docking and superposition tools, as well as more conventional rigid-body methods, to examine NAD binding to the catalytic subunits of diphtheria and pertussis toxins. Docking simulations with the rigid fragments adenine and nicotinamide revealed that the low energy dockings clustered in three distinct sites on the two proteins. Two of the sites were common to both fragments. The structures of the dinucleotides adenylyl 3'-5' uridine 3' monophosphate, and, more recently, NAD, bound to diphtheria toxin reveal that one pair of adenine/nicotinamide docking clusters is consistent with the two related complex structures. We chose adenine/nicotinamide pairs of dockings from these clusters, and superimposed flexible models of NAD onto these pairs. A Monte Carlo-based flexible docking procedure and energy minimization were used to refine the modeled NAD-PT complexes. The modeled complexes account for sequence similarities between PT and DT, and are consistent with many results that suggest the catalytic importance of certain residues.