Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization†

The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models. Our MD simulation results show that GTP binding significantly enhances the conformational flexibility of KRAS, and thus promotes its transition to an active conformation with more open switch I and II regions. MSMs analyses show that KRAS in the GTP-bound state can be transitioned to the active state more efficiently during the simulation than in the GDP-bound state. In addition, NRI model calculations showed that GTP binding enhanced residue–residue interactions within the KRAS protein, especially when the long-range interactions were significantly enhanced. Furthermore, the allosteric signaling pathways from the P-loop to switch I and II as well as the key amino acid sites along the pathways were obtained using a graph-based shortest path analysis. Our results can contribute to a deeper understanding of the mechanism of KRAS allosteric activation and provide a foundation for the development of targeted therapeutic drugs to regulate KRAS activity.