The proton transfer mechanism of the Ras GTPases, the effect of the GTPase activating protein, and oncogenic mutations

Ras-positive cancer constitutes a major challenge for medical treatment. Ras is a central protein in the RAF/MAPK signaling pathway and mutational hot spot residues Gly12, Gly13 and Gln61 constitute the majority of oncogenic mutations which are associated with detrimental clinical prognosis. To target the aberrant signaling by directly interfering with the Ras activity, one must have a thorough understanding of the mechanism of GTP hydrolysis. We employed ab initio calculations and QM/MM enhanced sampling methods to study the possible pathways, with a particular focus on the proton transfer steps. One important requirement for a feasible mechanism is to be consistent with the activating role of the GTPase activating protein (GAP) as well as the disabling nature of key oncogenic mutations of the Ras. Our model successfully recovers the GAP activation and the decreased rate of hydrolysis in Ras mutants. The thus obtained data on the mechanism can be the foundation of a virtual screening procedure designed to find ways of modulating mutant Ras activity.