Analysis of Water Molecules in the Hras-GTP and GDP Complexes with Molecular Dynamics Simulations

  • Takeshi Miyakawa
  • Ryota Morikawa
  • Masako Takasu
  • Akira Dobashi
  • Kimikazu Sugimori
  • Kazutomo Kawaguchi
  • Hiroaki Saito
  • Hidemi Nagao
Conference paper
Part of the Progress in Theoretical Chemistry and Physics book series (PTCP, volume 27)

Abstract

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.

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Copyright information

© Springer International Publishing Switzerland 2013

Authors and Affiliations

  • Takeshi Miyakawa
    • 1
  • Ryota Morikawa
    • 1
  • Masako Takasu
    • 1
  • Akira Dobashi
    • 2
  • Kimikazu Sugimori
    • 3
  • Kazutomo Kawaguchi
    • 4
  • Hiroaki Saito
    • 4
  • Hidemi Nagao
    • 4
  1. 1.School of Life SciencesTokyo University of Pharmacy and Life SciencesHachiojiJapan
  2. 2.School of PharmacyTokyo University of Pharmacy and Life SciencesHachiojiJapan
  3. 3.Research Center for Higher EducationKanazawa UniversityKanazawaJapan
  4. 4.Institute of Science and EngineeringKanazawa UniversityKanazawaJapan

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