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Related Experiment Videos

Raman difference studies of GDP and GTP binding to c-Harvey ras

J H Wang1, D G Xiao, H Deng

  • 1Department of Physics, The City College of the City University of New York 10031, USA.

Biochemistry
|August 7, 1998
PubMed
Summary

Investigating guanosine diphosphate (GDP) and guanosine triphosphate (GTP) binding to the Harvey-Ras protein reveals key structural changes. These findings illuminate the mechanism of GTP hydrolysis, crucial for cellular signaling.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • The Harvey-Ras protein (Ras) is a key regulator of cellular signaling pathways.
  • Understanding the mechanism of GTP hydrolysis by Ras is critical for deciphering its function and dysfunction in diseases like cancer.

Purpose of the Study:

  • To elucidate the structural and dynamic changes of guanosine diphosphate (GDP) and guanosine triphosphate (GTP) upon binding to the c-Harvey p21(ras) protein.
  • To investigate the role of active site interactions and water molecules in facilitating GTP hydrolysis.

Main Methods:

  • 18O isotope edited Raman difference spectroscopy was employed to analyze the vibrational spectra of GDP and GTP bound to Ras.
  • Ab initio calculations and empirical relationships were used to analyze frequency shifts and relate them to bond orders and lengths.

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  • Molecular modeling was used to study interactions within the nucleotide binding site.

    • Main Results:

    • Phosphate vibrational frequencies change significantly upon GDP/GTP binding to Ras.
    • Bound GDP is stabilized by electrostatic interactions with Mg2+.
    • Bound GTP exhibits altered gamma-phosphate geometry, approaching planarity, indicative of a transition state.
    • A water molecule positioned in-line with the P-O bond forms a weak bond with the gamma-phosphorus, weakening the leaving group bond.

    Conclusions:

    • The active site structure of Ras strategically positions an in-line water molecule to facilitate GTP hydrolysis.
    • Ras-bound GTP undergoes structural changes consistent with a synchronous bond formation and breaking mechanism during hydrolysis.
    • These findings provide insights into the reaction pathway of GTP hydrolysis in Ras, relevant to its signaling function.