分子模型揭示了Ras-GAP催化鸟苷三磷酸水解机理的多样性。,Organic & Biomolecular Chemistry

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分子模型揭示了Ras-GAP催化鸟苷三磷酸水解机理的多样性。
Organic & Biomolecular Chemistry ( IF 2.9 ) Pub Date : 2019-05-15 , DOI: 10.1039/c9ob00463g
Bella L Grigorenko ₁ , Ekaterina D Kots , Alexander V Nemukhin

Affiliation

由细胞蛋白Ras催化的鸟苷三磷酸（GTP）水解与活化蛋白GAP结合的看似简单的反应机理是一个重要的问题，因为该反应在癌症研究中具有重要意义。我们显示，在Ras-GAP活性位点的GTP水解的分子模型揭示了取决于在野生型酶中谷氨酰胺占据的Ras中61位置上分子组的内在化学反应机制的多样性。首先，在量子力学/分子力学（QM / MM）级别计算的反应能谱的比较表明，野生型Ras中Gln61侧链分配给QM或分配给MM部件会导致与谷氨酰胺辅助或底物辅助机制。第二，在实验研究中应用的谷氨酰胺（NGln）的硝基类似物或Glu取代Gln61，导致了另外两种以所谓的双水和协同型机理为特征的场景。野生型Ras-GAP中的谷氨酰胺辅助机制（其中保守的Gln61起决定性作用，在酰胺和酰亚胺互变异构体形式之间切换）与已知的结构，动力学和光谱研究实验结果一致。结果强调了Ras残基Gln61在Ras-GAP催化中的作用，并解释了Ras-GAP复合物在Ras的Gln61NGln和Gln61Glu突变体中保留的对GTP水解的催化活性。野生型Ras-GAP中的谷氨酰胺辅助机制（其中保守的Gln61起决定性作用，在酰胺和酰亚胺互变异构体形式之间切换）与已知的结构，动力学和光谱研究实验结果一致。结果强调了Ras残基Gln61在Ras-GAP催化中的作用，并解释了Ras-GAP复合物在Ras的Gln61NGln和Gln61Glu突变体中保留的对GTP水解的催化活性。野生型Ras-GAP中的谷氨酰胺辅助机制（其中保守的Gln61起决定性作用，在酰胺和酰亚胺互变异构体形式之间切换）与已知的结构，动力学和光谱研究实验结果一致。结果强调了Ras残基Gln61在Ras-GAP催化中的作用，并解释了Ras-GAP复合物在Ras的Gln61NGln和Gln61Glu突变体中保留的对GTP水解的催化活性。

"点击查看英文标题和摘要"

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling.

The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the activating protein GAP is an important issue because of the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis in the Ras-GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM) level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type mechanisms. The glutamine-assisted mechanism in the wild-type Ras-GAP, in which the conserved Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the role of the Ras residue Gln61 in Ras-GAP catalysis and explain the retained catalytic activity of the Ras-GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.

更新日期：2019-05-16

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