Analysis of Water Molecules in the Hras-GTP and GDP Complexes with Molecular Dynamics Simulations
In the Hras-GTP and GDP complexes, the coordination bonds between Mg2+ and oxygen atoms are very important. In this study, we use AMBER03 and our calculated force field parameters, and perform MD simulations of Hras-GTP and GDP complexes with water solvents. It is shown that the number of water molecules in the first hydration sphere is larger in GDP than in GTP. The duration time and the direction of water molecules in the first hydration sphere in GTP is not so different from those in GDP. It is shown that water molecules are distributed evenly around PG, although they are not distributed evenly around PB. This difference can be the reason why the hydrolysis of GTP in Hras-GTP is easier than the hydrolysis of GDP in Hras-GDP.
KeywordsWater Molecule Angular Distribution Duration Time Radial Distribution Function Phosphorus Atom
This work was supported by JSPS KAKENHI Grant Number 24540442. The computations were in part carried out at the Research Center for Computational Science, Okazaki, Japan.
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