The Potentials of the Atoms around Mg2+ in the H-ras GTP and GDP Complexes

  • T. Miyakawa
  • R. Morikawa
  • M. Takasu
  • K. Sugimori
  • K. Kawaguchi
  • H. Saito
  • H. Nagao
Conference paper
Part of the Progress in Theoretical Chemistry and Physics book series (PTCP, volume 26)

Abstract

We have studied the quantum state around the Mg2+ ion in the H-ras GTP and H-ras GDP complexes in order to understand the hydrolysis of GTP to GDP in the H-ras complex, which plays a key role in overcoming human cancer. We calculated the force fields and atomic charges around the Mg2+ ion in the H-ras GTP and H-ras GDP complexes at the B3LYP level, using a basis functional set 6-31G**. The calculations were performed in the subsystem consisting of the bases or the molecules containing the oxygen having a coordinate bond to the Mg2+ ion. They showed that the oxygen atoms in both GTP and GDP bind tightly to the Mg2+ ion, although the oxygen atoms in H2O bind loosely. We have also performed MD simulations of the H-ras GTP and H-ras GDP complexes in solution, using these potential parameters. We showed that the structure differences between H-ras GTP and H-ras GDP are found mainly in loop 2 and loop 4.

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Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • T. Miyakawa
    • 1
  • R. Morikawa
    • 1
  • M. Takasu
    • 1
  • K. Sugimori
    • 2
  • K. Kawaguchi
    • 3
  • H. Saito
    • 3
  • H. Nagao
    • 3
  1. 1.School of Life SciencesTokyo University of Pharmacy and Life SciencesHachioji, TokyoJapan
  2. 2.Department of Physical Therapy, Faculty of Health SciencesKinjo UniversityHakusanJapan
  3. 3.Institute of Science and EngineeringKanazawa UniversityKakuma, KanazawaJapan

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