Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

• Reacting species upon GTP hydrolysis by the Ras-GAP protein system were analyzed.
• Vibrational spectra of intermediates were characterized in QM/MM calculations.
• Computed and observed FTIR vibrational bands of intermediates were compared.

The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.

Vibrational analysis of the reactants and the reaction intermediates upon the GTP + H2O → GDP + Pi transformations inside the Ras-GAP enzyme complex is carried out following the QM/MM calculations of the elementary stages of the enzyme reaction. Comparison of the computed and observed vibrational frequencies provides a strong support to the reaction mechanism for the GTP hydrolysis in this system at the atomic level. Evolution of the characteristic vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.Figure optionsDownload as PowerPoint slide