Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics
Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics
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DOI：
10.1021/bi901353v
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发表时间：
2009-11-10
期刊：
影响因子：
2.9
通讯作者：
Hammes-Schiffer, Sharon
中科院分区：
文献类型：
--
作者：
Chakravorty, Dhruva K.;Soudackov, Alexander V.;Hammes-Schiffer, Sharon
本文介绍了对酮类固醇异构酶催化的两个质子转移反应进行的混合量子/经典分子动力学模拟。采用经验价键法描述了质子转移反应的势能面。转移氢的核量子效应使速率提高了约8倍，而动态势垒重交叉使速率降低了3 - 4倍。对于这两个质子转移反应，供体 - 受体距离在过渡态时大幅减小。天冬氨酸38（Asp38）侧链的羧酸盐基团在第一步和第二步中分别作为质子受体和供体，在两个质子转移反应之间发生显著旋转。活性位点内的氢键相互作用与天冬氨酸99（Asp99）和酪氨酸14（Tyr14）与底物的氢键作用相符。模拟表明，天冬氨酸99与底物之间的氢键从第一个质子转移步骤开始就存在，而酪氨酸14与底物之间的氢键在该步骤的前期几乎不存在，但在过渡态形成时几乎同时形成。在整个第二个质子转移步骤中，这两种氢键都存在，直到产物部分解离。酪氨酸14和酪氨酸55之间的氢键在两个质子转移步骤中都存在。活性位点残基在第一步比在第二步更具流动性。底物与酶之间的范德华相互作用能沿反应路径几乎保持不变，但是，烯醇化物中间体的静电相互作用能比反应物和产物的要强得多。活性位点远端的移动环区域在催化反应过程中表现出显著的结构重排，在某些情况下，静电势发生质的变化。这些结果表明，酶活性位点和底物相对较小的构象变化增强了稳定中间体的氢键，从而促进了质子转移反应。此外，与这些反应相关的构象和静电变化不限于活性位点，而是延伸到整个酶。
Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a Factor of similar to 8, and dynamical barrier recrossings decrease the rates by a factor of 3-4 For both proton transfer reactions, the donor-acceptor distance decreases substantially Lit the transition state The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps. respectively, rotates significantly between the two proton transfer reactions. The hydrogen-bonding interactions within the active site are Consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate The simulations suggest that I hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals Interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathmay, bill. the electrostatic Interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangement and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the Intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme.