Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis.

Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard to mutation-mediated tuning on the activity of K-Ras, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations followed by analysis of free energy landscapes (FELs) are performed on the GDP- and GTP-bound wild-type (WT), G12V, and D33E K-Ras. The results suggest that G12V and D33E not only evidently change the flexibility of SW1 and SW2 but also greatly affect correlated motions of SW1 and SW2 separately relative to the P-loop and SW1, which exerts a certain tuning on the activity of K-Ras. The information stemming from the analyses of FELs reveals that the conformations of SW1 and SW2 are in high disorders in the GDP- and GTP-associated WT and mutated K-Ras, possibly producing significant effect on binding of guanine nucleotide exchange factors or effectors to K-Ras. The interaction networks of GDP and GTP with K-Ras are identified and the results uncover that the instability in hydrogen-bonding interactions of SW1 with GDP and GTP is mostly responsible for conformational disorder of SW1 and SW2 as well as tunes the activity of oncogenic K-Ras.