Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis

The GTPase superfamily of enzymes that hydrolyze GTP have a number of conserved sequence regions (the so-called “Gmotifs”), and several of the subfamilies also require catalytic activation by specific GTPase-activating proteins. In the translational GTPases involved in protein synthesis, this activating function is instead accomplished by their interaction with the ribosome. Despite these similarities, there are distinct differences regarding some of the amino acid residues making up the GTPase active sites. This raises the question of whether or not the catalytic mechanisms of different types of GTPases are identical. We report herein extensive computer simulations of both the intrinsic GTP hydrolysis reaction of Ras and the considerably faster reaction activated by the interaction with RasGAP. The results of these calculations are compared to earlier simulations of GTP hydrolysis by EF-Tu on the ribosome and show that the favored reaction pathways are strongly dependent on the composition of the active site. By computing Arrhenius plots for the temperature dependence of the calculated free energy profiles, we further show that different mechanistic pathways are associated with distinct differences in activation entropies and enthalpies. The activation parameters are in good agreement with experimental data, and we conclude that calculations of Arrhenius plots from computer simulations can be very useful for dissecting the energetics of enzyme catalysis.