Section 22.1.2.4.1.4.  GRASP surfaces

GRASP is currently perhaps the most popular program for the display of molecular surfaces. Readers are referred to the program documentation (Nicholls, 1992) or a paper that tangentially describes an early implementation (Nicholls et al., 1991). The molecular or accessible surface is determined by the marching-cube algorithm. The surface is filled using methods that make modest compromises on photorealistic light reflection etc., but take advantage of machine-dependent Silicon Graphics surface rendering to perform the display fast enough for interactive adjustment of the view.

The most powerful part of the program is the ability to colour according to properties mapped to the surface (see Fig. 22.1.2.2). These may be values of (say) electrostatic potential interpolated from a three-dimensional lattice. Much has been learned about many proteins from the potentials determined by solution of the Poisson–Boltzmann equation (Nicholls & Honig, 1991). The electrostatic complementarity of binding surfaces has often been readily apparent in ways that were not obvious from Coulombic calculations that ignore screening or from calculations and graphics representations that treat the charges of individual atoms as independent entities.

Figure 22.1.2.2 | top | pdf | GRASP example. The larger picture shows the molecular surface of arginine kinase (Zhou et al., 1998) with the domains and a loop moved to the open configuration seen in a homologous creatine kinase structure (Fritz-Wolf et al., 1996). The surface, coloured with positive charge blue and negative charge red, demonstrates that the active-site pocket (centre) is the most positively charged part of the structure. It complements the negatively charged phosphates of the transition-state analogue components that are shown, moved as a rigid body to the bottom right. They are shown in van der Waals representation, in which oxygens are red, carbons black and nitrogens blue.

Many other properties can be mapped to the surface. These include properties of the atoms associated with that part of the surface (such as thermal factors), curvature of the surface calculated from adjacent atoms (Nicholls & Honig, 1991), or distance to the nearest part of the surface of an adjacent molecule. GRASP is now used to illustrate complicated molecular structures, in part because it also supports the superimposition of other objects over the molecular surface. These include the representation of molecules with CPK spheres and/or bonds, and the representation of electrostatic potentials with field lines, dipole vectors etc.