VALIDATION OF THE USE OF INTERMOLECULAR NOE CONSTRAINTS FOR OBTAININGDOCKED STRUCTURES OF PROTEIN-LIGAND COMPLEXES

The use of intermolecular NOEs for docking a small ligand molecule int o its target protein has been investigated with the aim of determining the effectiveness and methodology of this type of NOE docking calcula tion. A high-resolution X-ray structure of a protein-ligand complex ha s been used to simulate loose distance constraints of varying degrees of quality typical of those estimated from experimental NOE intensitie s. These simulated data were used to examine the effect of the number, distribution and representation of the experimental constraints on th e precision and accuracy of the calculated structures. A standard simu lated annealing protocol was used, as well as a more novel method base d on rigid-body dynamics. The results showed some analogies with those from similar studies on complete protein NMR structure determinations , but it was found that more constraints per torsion angle are require d to define docked structures of similar quality. The effectiveness of different NOE-constraint averaging methods was explored and the benef its of using 'R(-6) averaging' rather than 'centre averaging' with sma ll sets of NOE constraints were shown. The starting protein structure used in docking calculations was obtained from previous X-ray or NMR s tructure studies on a related complex. The effects on the calculated c onformations of introducing structural differences into the binding si te of the initial protein structure were also considered.