Quantitative exploration of the molecular origin of the activation of GTPase
Quantitative exploration of the molecular origin of the activation of GTPase
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DOI：
10.1073/pnas.1319854110
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发表时间：
2013-11
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影响因子：
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通讯作者：
Ram Prasad B;N. V. Plotnikov;J. Lameira;A. Warshel
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文献类型：
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作者：
Ram Prasad B;N. V. Plotnikov;J. Lameira;A. Warshel
意义-GTP酶的激活的起源进行了探讨，考虑到参考溶液反应的过渡态涉及两个水分子之间的质子转移的证据。基于从头算量子力学/分子力学的经验价键表面的溶液反应的校准被用来模拟GTbenzene活化过程。的激活被发现反映了相同类型的静电稳定先前获得的单水机制。过渡态质子转移步骤似乎不是速率限制的，因此与催化效果无关。计算的RasGAP和EF-Tu的活化定量再现了观察到的趋势，并确定了其变构起源。我们相信我们的发现对所有GTP酶都是通用的。GTP酶在细胞过程中发挥着重要作用，获得对其激活的定量理解需要溶液中相关机制路径的可靠自由能表面，以及将此信息插值到GTP酶。最近，我们生成了溶液中磷酸单酯水解的从头算量子力学/分子力学自由能表面，定量地确定了来自单个攻击水（1 W）的质子转移（PT）步骤的反应的势垒高于第二水（2 W）辅助PT的反应。这一发现对GTP酶的激活的影响是量化的，在这里，通过使用从头算溶液表面校准经验价键表面，然后探索的激活效应的起源。结果表明，虽然2 W PT路径是一个新元素，但这一步并不是速率决定步骤，催化效应实际上是由于PT前过渡态的静电稳定和随后的平台效应.因此，我们之前在1 W机制下对Ras GTPase激活蛋白（RasGAP）和延伸因子Tu（EF-Tu）的研究中发现的静电催化效应对于2 W路径仍然有效。此外，如前所述，相应的激活似乎涉及主要的变构效应。总的来说，我们认为我们的发现对GTP酶和ATP酶都是通用的。除了生物学相关的发现，我们还提供了一个关键的讨论，从可靠的表面酶促反应的要求。
Significance The origin of the activation of GTPases is explored considering the evidence that the transition state for the reference solution reaction involves a proton transfer between two water molecules. Ab initio quantum mechanical/molecular mechanical–based calibration of empirical valence bond surfaces of the solution reaction is used to simulate the GTPase activation process. The activation is found to reflect the same type of electrostatic stabilization obtained previously for the single water mechanism. The transition state proton transfer step does not appear to be rate limiting and thus is irrelevant to the catalytic effect. The calculated activation of RasGAP and EF-Tu reproduce the observed trend quantitatively and establishes its allosteric origin. We believe that our finding is general to all GTPases. GTPases play a major role in cellular processes, and gaining quantitative understanding of their activation demands reliable free energy surfaces of the relevant mechanistic paths in solution, as well as the interpolation of this information to GTPases. Recently, we generated ab initio quantum mechanical/molecular mechanical free energy surfaces for the hydrolysis of phosphate monoesters in solution, establishing quantitatively that the barrier for the reactions with a proton transfer (PT) step from a single attacking water (1W) is higher than the one where the PT is assisted by a second water (2W). The implication of this finding on the activation of GTPases is quantified here, by using the ab initio solution surfaces to calibrate empirical valence bond surfaces and then exploring the origin of the activation effect. It is found that, although the 2W PT path is a new element, this step is not rate determining, and the catalytic effect is actually due to the electrostatic stabilization of the pre-PT transition state and the subsequent plateau. Thus, the electrostatic catalytic effect found in our previous studies of the Ras GTPase activating protein (RasGAP) and the elongation factor-Tu (EF-Tu) with a 1W mechanism is still valid for the 2W path. Furthermore, as found before, the corresponding activation appears to involve a major allosteric effect. Overall, we believe that our finding is general to both GTPases and ATPases. In addition to the biologically relevant finding, we also provide a critical discussion of the requirements from reliable surfaces for enzymatic reactions.