Fragment-based modeling of NAD binding to the catalytic subunits of diphtheria and pertussis toxins

We describe a novel application of a fragment-based ligand docking technique; similar methods are commonly applied to the de novo design of ligands for target protein binding sites. We have used several new flexible docking and superposition tools, as well as a more conventional rigid-body (fragment) docking method, to examine NAD binding to the catalytic subunits of diphtheria (DT) and pertussis (PT) toxins, and to propose a model of the NAD-PT complex. Docking simulations with the rigid NAD 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 and were related to the structure of NAD bound to DT in an obvious way; however, the adenine subsite of PT was shifted relative to that of DT. We chose adenine/nicotinamide pairs of PT dockings from these clusters and flexibly superimposed 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 complex accounts for the sequence and structural similarities between PT and DT and is consistent with many results that suggest the catalytic importance of certain residues. A possible functional role for the structural difference between the two complexes is discussed.