Computational modeling of the catalytic reaction in triosephosphate isomerase
Computational modeling of the catalytic reaction in triosephosphate isomerase
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DOI：
10.1016/j.jmb.2003.11.016
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发表时间：
2004-03-12
影响因子：
5.6
通讯作者：
Friesner, RA
中科院分区：
文献类型：
--
作者：
Guallar, V;Jacobson, M;Friesner, RA
我们提出了一个全面的分析磷酸丙糖异构酶（TIM）的催化循环，包括反应化学和催化环和侧链运动。结合精确的混合量子力学/分子力学（QM/MM）和蛋白质结构预测方法，我们模拟了二羟基丙酮磷酸（DHAP）可逆异构化为D-甘油醛3-磷酸（GAP）的结构和化学方面，其中有丰富的实验数据。这种新的计算方法与使用最近的近原子分辨率TIM-DHAP米氏络合物PDB结构，1NEY.PDB的结合，使我们能够获得强大的定性，并在可用的情况下，定量协议与广泛的实验数据。我们能够得出的主要结论之一是单阴离子的重要性，（与双阴离子相反）形式的底物磷酸基团在催化循环中，活性位点中关键催化残基的详细定位和能量学，Glu 165的柔性性质，这有利于其直接参与包被中间体的形成，在存在和不存在底物的情况下催化环区域的开放和闭合形式的能量学，以及各种实验测量的反应速率的定量再现，通常在类似于1千卡/摩尔内。我们的结果与现有的实验数据是一致的，并提供了一个初步的图片，为什么环开放时，GAP的产品具有更高的障碍比当DHAP的产品。(C)2003 Elsevier Ltd.保留所有权利。
We present a comprehensive analysis of the catalytic cycle of the enzyme triosephosphate isomerase (TIM), including both the reactive chemistry and the catalytic loop and side-chain motions. Combining accurate mixed quantum mechanics/molecular mechanics (QM/MM) and protein structure prediction methods, we have modeled both the structural and, chemical aspects of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde 3-phosphate (GAP), for which there is a wealth of experimental data. The conjunction of this novel computational approach with the use of the recent near-atomic resolution TIM-DHAP Michaelis complex PDB structure, 1NEY.pdb, has enabled us to obtain robust qualitative and, where available, quantitative agreement with a wide range of experimental data. Among the principal conclusions that we are able to draw are the importance of the monoanionic (as opposed to dianioic) form of the substrate phosphate group in the catalytic cycle, detailed positioning and energetics of the key catalytic residues in the active-site, the flexible nature of Glu165, which favors its direct involvement in the formation of the enediol intermediate, energetics of the open and closed form of the catalytic loop region in the presence and absence of substrate, and quantitative reproduction of various experimentally measured reaction rates, typically to within similar to1 kcal/mol. Our results are consistent with the available experimental data, and provide an initial picture as to why loop opening when GAP is the product has a higher barrier than when DHAP is the product. (C) 2003 Elsevier Ltd. All rights reserved.