How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab initio QM/MM study
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: An ab initio QM/MM study
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DOI：
10.1021/ja0464084
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发表时间：
2005-02-09
影响因子：
15
通讯作者：
McCammon, JA
中科院分区：
文献类型：
--
作者：
Cheng, YH;Zhang, YK;McCammon, JA
我们对cAMP依赖性蛋白激酶（PKA）催化亚基进行了密度泛函理论QM/MM计算。QM/MM计算结果表明，PKA催化的磷酸化反应主要为解离反应，Asp 166作为催化碱接受底物肽传递的质子.在活性中心的关键相互作用中，发现Mg 2+离子、富含甘氨酸的环和Lys 72通过静电相互作用稳定过渡态。另一方面，赖氨酸168，天冬氨酸171，天冬氨酸184，和保守的沃茨结合到镁离子不直接有助于降低磷酸化反应的能量势垒，并提出了这些残基的可能作用。用不同的QM/MM分配方案或不同的初始结构进行QM/MM计算，得到了一致的结果。此外，我们已经进行了12 ns的分子动力学模拟野生型和K168 A突变的PKA，分别证明，Lys 168的催化作用是保持ATP和底物肽在近攻击反应构象。
We have carried out density functional theory QM/MM calculations on the catalytic subunit of cAMP-dependent protein kinase (PKA). The QM/MM calculations indicate that the phosphorylation reaction catalyzed by PKA is mainly dissociative, and Asp166 serves as the catalytic base to accept the proton delivered by the substrate peptide. Among the key interactions in the active site, the Mg2+ ions, glycine rich loop, and Lys72 are found to stabilize the transition state through electrostatic interactions. On the other hand, Lys168, Asn171, Asp184, and the conserved waters bound to Mg2+ ions do not directly contribute to lower the energy barrier of the phosphorylation reaction, and possible roles for these residues are proposed. The QM/MM calculations with different QM/MM partition schemes or different initial structures yield consistent results. In addition, we have carried out 12 ns molecular dynamics simulations on both wild type and K168A mutated PKA, respectively, to demonstrate that the catalytic role of Lys168 is to keep ATP and substrate peptide in the near-attack reactive conformation.