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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols
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Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols

机译：来自协议等级的蛋白氯化物氧化酶的理论模型

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摘要

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm(-1) red shift of the C-13(1) carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q(x) electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.
机译：酶偶氯化酶氧化还原酶（LPOR）催化氯化氯化物（PCHLIDE）的光驱动减少，叶绿素生物合成中的关键步骤。对光催化机制的LPOM的分子理解对于利用光能来介导酶促反应是必不可少的。没有X射线晶体结构促进了LPOR同源型模型的发育，缺乏催化竞争力的活性位点，无法解释各种报告的光谱证据，包括时间分辨光学光谱数据。我们已经改进了先前的结构模型，以考虑催化活性位点和钯结合的特征实验光谱特征，包括中红外线（1）羰基拉伸振动的26cm（-1）红色移位（ IR）和Q（x）电子频带的12nm红色移位。理论方法的层次结构，包括同源性建模，分子动力学模拟，混合量子力学[（TD-）DFT] /分子力学[琥珀]计算，以及计算振动和电子光谱，并在迭代方案中组合以再现实验证据并预测与催化过程相关的超快瞬时IR光谱指纹。对LOS酶的成功应用表明，所提出的分层协议为蛋白质结构细化提供了一般的工作流程。

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