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 tec hnique; similar methods are commonly applied to the de novo design of ligands for target protein binding sites, We have used several new fle xible docking and superposition tools, as well as a more conventional rigid-body (fragment) docking method, to examine NAD binding to the ca talytic subunits of diphtheria (DT) and pertussis (PT) toxins, and to propose a model of the NAD-PT complex, Docking simulations with the ri gid NAD fragments adenine and nicotinamide revealed that the low-energ y dockings clustered in three distinct sites on the two proteins. Two of the sites were common to both fragments and were related to the str ucture of NAD bound to DT in an obvious way; however, the adenine subs ite of PT was shifted relative to that of DT. We chose adenine/nicotin amide pairs of PT dockings from these clusters and flexibly superimpos ed NAD onto these pairs. A Monte Carlo-based flexible docking procedur e and energy minimization were used to refine the modeled NAD-PT compl exes. The modeled complex accounts for the sequence and structural sim ilarities between PT and DT and is consistent with many results that s uggest the catalytic importance of certain residues. A possible functi onal role for the structural difference between the two complexes is d iscussed. (C) 1998 Wiley-Liss, Inc.