The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations

Abstract

The coordination of the magnesium ion in proteins by triphosphates plays an important role in catalytic hydrolysis of GTP or ATP, either in signal transduction or energy conversion. For example, in Ras the magnesium ion contributes to the catalysis of GTP hydrolysis. The cleavage of GTP to GDP and P(i) in Ras switches off cellular signaling. We analyzed GTP hydrolysis in water, Ras, and Ras·Ras-GTPase-activating protein using quantum mechanics/molecular mechanics simulations. By comparison of the theoretical IR-difference spectra for magnesium ion coordinated triphosphate to experimental ones, the simulations are validated. We elucidated thereby how the magnesium ion contributes to catalysis. It provides a temporary storage for the electrons taken from the triphosphate and it returns them after bond cleavage and P(i) release back to the diphosphate. Furthermore, the Ras·Mg(2+) complex forces the triphosphate into a stretched conformation in which the β- and γ-phosphates are coordinated in a bidentate manner. In this conformation, the triphosphate elongates the bond, which has to be cleaved during hydrolysis. Furthermore, the γ-phosphate adopts a more planar structure, driving the conformation of the molecule closer to the hydrolysis transition state. GTPase-activating protein enhances these changes in GTP conformation and charge distribution via the intruding arginine finger.

Figure 1

Applied method: Using MM (50 ns) and QM/MM simulations (6 × 2.5-ps equilibration plus 0.5-ps evaluation), we computed different states during hydrolysis. The starting structures of the MM simulations are prepared x-ray structures in a water box with physiological sodium chloride concentration. As starting structures for QM/MM simulations, we took six snapshots, each 5 ns from the last 25 ns of the MM trajectory. After 2.5 ps of QM/MM simulation, vibrational modes were calculated for comparison with the experimental IR spectrum. The last 0.5 ps of the validated QM/MM trajectories were used for a detailed investigation of charge shifts and structural details of the substrate. This procedure is repeated for all six simulations systems (see Table S1 in the Supporting Material).

Figure 2

Coordination of GTP/GDP in Ras or Ras·GAP. The coordination partners of the GTP/GDP were estimated by the contact matrix algorithm of MAXIMOBY (41) from the 50-ns MM simulation. The bold-faced amino acids have contacts that occur during MM simulation but are not present in the x-ray structure (PDB:1QRA (18)). The italicized amino acids are contacts that are present in the x-ray structure but are not stable during MM simulation. The other amino acids have contacts in the x-ray structure that are stable during the MM simulation. Shown is the coordination of GTP in the open Ras·GTP·Mg²⁺ structure (a) in the absence of a hydrogen bond between Tyr³² and the γ-phosphate, and (b) with the formed hydrogen bond. (c) Coordination of GTP in Ras·GTP·Mg²⁺·GAP. (d) Coordination of GDP in Ras·GDP·Mg²⁺.

Figure 3

Comparison of calculated and measured vibrational modes for Ras·GTP·Mg²⁺ in water. (Light blue) Calculated vibrational modes from te Heesen et al. (13) based on the open structure. (Far-left side of the light-green shaded area) Our calculated results for the open structure. (Far-right side of the light-green shaded area) Calculated results based on the closed structure. (Light-yellow shaded area) Measured vibrational modes of Allin et al. (39). A detailed list of all calculated vibrational modes for all simulation systems is provided in Table S2.

Figure 4

Partial charge shifts during hydrolysis. An electron shift to the magnesium ion occurs before hydrolysis, which is reverted by the bond cleavage and P_i release. The charge shifts result from differences in the charges relative to the previous state starting from GTP in water without a magnesium ion. (a–c) Changes in the precatalytic states, (d) towards the intermediate state and (e) towards the product state. The charges of each state are described in Table S3. All charge shifts are given in the unit of the electron charge e₀. (Arrows) Direction in which electrons are transferred.

Figure 5

Structural changes of GTP·Mg²⁺ in water bound to Ras and Ras·GAP. Structural changes accompany the charge shifts. These changes lead to a destabilization of the educt state and lower the barrier for hydrolysis; this already occurs in the precatalytic state. Changes are exaggerated for clarity.