Department of Biophysics, Ruhr-University Bochum, Bochum, Germany.
Biophys J. 2012 Jul 18;103(2):293-302. doi: 10.1016/j.bpj.2012.06.015. Epub 2012 Jul 17.
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.
三磷酸与蛋白质中镁离子的配位对 GTP 或 ATP 的催化水解（无论是在信号转导还是能量转换中）起着重要作用。例如，在 Ras 中，镁离子有助于 GTP 水解的催化。GTP 裂解为 GDP 和 P(i)会关闭细胞信号。我们使用量子力学/分子力学模拟分析了水中、Ras 以及 Ras·Ras-GTPase-activating protein 中的 GTP 水解。通过将理论红外差光谱与实验的镁离子配位三磷酸进行比较，对模拟进行了验证。从而阐明了镁离子如何促进催化。它为从三磷酸中获得的电子提供了临时存储，并在键断裂和 P(i)释放后将其返回到二磷酸酯。此外，Ras·Mg(2+) 复合物将三磷酸拉长，使β-和γ-磷酸以双齿配位方式配位。在这种构象中，三磷酸拉长了在水解过程中必须断裂的键。此外，γ-磷酸采用更平面的结构，使分子的构象更接近水解过渡态。GTPase-activating protein 通过侵入的精氨酸指增强了 GTP 构象和电荷分布的这些变化。
