The
Ras protein is one of the most important drug targets for battling
cancers. To effectively design novel drugs of Ras, we characterize
here its conformational ensembles for the hydrolysis intermediate
state RasGDP·Pi and the product state RasGDP by extensive replica-exchange
molecular dynamics simulations. Several substates for RasGDP·Pi
have been identified, while structural analyses have revealed an unrecognized
hydrogen-bonding network that stabilizes the hydrolysis intermediate
state. More interestingly, Gln61, which is involved in numerous oncogenic
mutations, was found to be engaged in this hydrogen-bonding network,
adopting a specific conformation that always points to Pi in contrast
to that in the RasGTP state. The simulations also reveal that RasGDP
has more than one substate, suggesting a conformational selection
mechanism for the interaction between Ras and the guanine nucleotide
exchange factors (GEFs). These findings offer new opportunities for
the drug design of Ras by stabilizing the hydrolysis intermediate
or disrupting its interaction with the GEFs.