CHARACTERIZATION OF PROTEIN-LIGAND INTERFACES - SEPARATING SURFACES

A new method for characterising protein-protein complexes is presented wherein the interface is modelled as a separating surface. This surfa ce is defined by a set of points located halfway on the shortest dista nce vectors between surface points of the two molecular partners. The surface is generated using a grid-based algorithm. The distance to the nearest atom is stored on the grid points and an isosurface is genera ted forming the separating surface. Size and shape of the surface char acterises the complex interface. Distances, forces, and other physicoc hemical properties can be mapped onto the surface and are used to stud y the intermolecular interactions. This is demonstrated with the syste ms lysozym-antibody, p53-DNA and trypsin-BPTI.