Molecular dynamics simulations of Gly-12-->Val mutant of p21(ras): dynamic inhibition mechanism.

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 H2O 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.

[1]  C. Hall,et al.  Regulation of Phosphorylation Pathways by p21 GTPases , 1996 .

[2]  W. Kabsch,et al.  The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. , 1997, Science.

[3]  Mark S. Boguski,et al.  Proteins regulating Ras and its relatives , 1993, Nature.

[4]  W. Kabsch,et al.  Refined crystal structure of the triphosphate conformation of H‐ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. , 1990, The EMBO journal.

[5]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[6]  A. Wittinghofer,et al.  Mutational and kinetic analyses of the GTPase-activating protein (GAP)-p21 interaction: the C-terminal domain of GAP is not sufficient for full activity , 1992, Molecular and cellular biology.

[7]  A. Wittinghofer,et al.  Aluminium fluoride associates with the small guanine nucleotide binding proteins , 1997, FEBS letters.

[8]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[9]  S H Kim,et al.  Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. , 1992, Science.

[10]  P. Schultz,et al.  Probing the structure and mechanism of Ras protein with an expanded genetic code. , 1993, Science.

[11]  W. Kabsch,et al.  Three-dimensional structures of H-ras p21 mutants: Molecular basis for their inability to function as signal switch molecules , 1990, Cell.

[12]  N. Futatsugi,et al.  Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21. , 1999, Biophysical journal.

[13]  M. Parrini,et al.  A New Function of p120-GTPase-activating Protein , 1997, The Journal of Biological Chemistry.

[14]  D. Herschlag,et al.  Ras-catalyzed hydrolysis of GTP: a new perspective from model studies. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[15]  R. Weinberg,et al.  Passage of phenotypes of chemically transformed cells via transfection of DNA and chromatin. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Takashi Amisaki,et al.  Development of MD Engine: High‐speed accelerator with parallel processor design for molecular dynamics simulations , 1999 .

[17]  Time-resolved crystallography on H-ras p21 , 1992, Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences.

[18]  W. Kabsch,et al.  Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation , 1989, Nature.