Molecular Dynamics Simulations of Gly-12→Val Mutant of p21 ras: Dynamic Inhibition Mechanism

Abstract

The mutant p21 ras protein is a G protein produced by the point-mutated H- ras gene, and this mutant protein has been shown to cause carcinogenesis due to a reduction in its GTPase activity. However, the mechanism underlying this strange phenomenon has still not been elucidated. In our previous study, we have clarified the mechanism of the GTP→GDP hydrolysis reaction in the wild-type p21 ras at the atomic level and concluded that GTPase-activating protein plays a significant role in the supply of H 2O molecules for the hydrolysis. The structure of the active site in the mutant is the same as that in the wild type. However, by performing molecular dynamic calculations, we found that the structure of the active site of the enzyme substrate complex in the oncogenic mutant p21 ras continuously changes, and these continuous changes in the active site would make it difficult for the GTP→GDP hydrolysis reaction to occur in the mutant. These findings can explain the fact that the GTPase activity in the mutant was only 15% of that in the wild type and the fact that GTPase-activating protein has no reaction-activating effect in the mutant. This is a dynamic inhibition mechanism of a vital reaction that can be explained by considering the molecular dynamics.