Identification of functional substates of KRas during GTP hydrolysis with enhanced sampling simulations

As the hub of major signaling pathways, Ras proteins are implicated in 19% of tumor-caused cancers due to perturbations in their conformational and/or catalytic properties. Despite numerous studies, the functions of the conformational substates for the most important isoform, KRas, remain elusive. In this work, we perform an extensive simulation analysis on the conformational landscape of KRas in its various chemical states during the GTP hydrolysis cycle: the reactant state KRasGTP center dot Mg2+, the intermediate state KRasGDP center dot Pi center dot Mg2+ and the product state KRasGDP center dot Mg2+. The results from enhanced sampling simulations reveal that State 1 of KRasGTP center dot Mg2+ has multiple stable substates in solution, one of which might account for interacting with GEFs. State 2 of KRasGTP center dot Mg2+ features two substates "Tyr32(in)" and "Tyr32(out)", which are poised to interact with effectors and GAPs, respectively. For the intermediate state KRasGDP center dot Pi center dot Mg2+, Gln61 and Pi are found to assume a broad set of conformations, which might account for the weak oncogenic effect of Gln61 mutations in KRas in contrast to the situation in HRas and NRas. Finally, the product state KRasGDP center dot Mg2+ has more than two stable substates in solution, pointing to a conformation-selection mechanism for complexation with GEFs. Based on these results, some specific inhibition strategies for targeting the binding sites of the high-energy substates of KRas during GTP hydrolysis are discussed.