The specific vibrational modes of GTP in solution and bound to Ras: a detailed theoretical analysis by QM/MM simulations

Abstract

The hydrolysis of guanosine triphosphate (GTP) in general, and especially by GTPases like the Ras protein, is in the focus of biological investigations. A huge amount of experimental data from Fourier-transformed infrared studies is currently available, and many vibrational bands of free GTP, GTP·Mg²⁺, and Ras·GTP·Mg²⁺ in solution have been assigned by isotopic labeling. In the Ras environment, bands between 800 cm⁻¹ and 1300 cm⁻¹ have already been assigned, but not those below 800 cm⁻¹. The combination of quantum and molecular mechanics (QM/MM) methods takes the quantum effects for selected relevant atoms into account. This provides structural details, vibrational frequencies and electron distributions of the region of interest. We therefore used MM and QM/MM simulations to investigate the normal vibrational modes of GTP, GTP·Mg²⁺, and Ras·GTP·Mg²⁺ in solution, and assigned the vibrational frequencies for each normal vibration mode. In this study, the quantum box contains the nucleoside and the Mg²⁺. The comparison of calculated and experimental vibrational spectra provides a very good control for the quality of the calculations. Structurally, MM and QM/MM simulations reveal a stable tridentate coordination of the Mg²⁺ by GTP in water, and a stable bidentate coordination by GTP in complex with Ras. For validation, we compare the calculated frequencies and isotopic shifts with the experimental results available in the range of 800 cm⁻¹ to 1300 cm⁻¹. For the first time we suggest band assignments of the vibrational modes below 800 cm⁻¹ by comparison of calculated and experimental spectra.