Mutation-Induced Effects on Rac1 Conformational Dynamics: Implications for Therapeutic Targeting

Understanding the conformational dynamics of proteins, particularly small GTPases like Rac1, is vital for elucidating their functional mechanisms and developing targeted therapies. Rac1, pivotal in cellular processes, toggles between inactive GDP-bound and active GTP-bound states, regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Mutations, such as Rac1’s spontaneously activating oncogenic gain-of-function mutation P29S, associated with cancer, disrupt this equilibrium, leading to aberrant signaling. Traditional drug targeting of Rac1 is challenging due to its biological complexity and the lack of accessible active sites on its surface, necessitating alternative strategies. We propose a computational framework integrating Molecular Dynamics (MD) simulations and Elastic Network Models (ENM) to explore conformational dynamics. Our findings highlight the interplay between Mg ²⁺ binding and conformational ensembles, revealing enhanced conformational heterogeneity in both inactive and active states upon P29S mutation. The critical location of P29S, Mg ²⁺ coordination site, and GDP/GTP binding pocket with respect to global hinges provides mechanistic insight into how this mutation disrupts normal protein function through altered metal coordination dynamics. Furthermore, we identified strategic positions as potential “ rescue mutation ” sites, with T75A showing particular promise in mitigating the destabilizing conformational effects of P29S. Overall, this work provides insights into Rac1’s dynamic behavior and offers a foundation for targeted drug design strategies.