Goodsell D S, Lauble H, Stout C D, Olson A J
Molecular Biology Institute, University of California, Los Angeles 90024.
Proteins. 1993 Sep;17(1):1-10. doi: 10.1002/prot.340170104.
Automated docking of substrates to proteins of known structure aids the process of crystallographic analysis in two ways. First, automated docking can be used to generate a small number of starting models for substrates using only protein coordinates from an early stage of refinement. Second, automated docking provides a method for exploring aspects of catalysis that are inaccessible to crystallography by postulating binding modes of catalytic intermediates. This paper describes the use of automated docking to explore the binding of substrates to aconitase. The technique starts with a substrate molecule in an arbitrary configuration and position and finds favorable docked configurations in a (static) protein active site based on a molecular mechanics type force field. Using protein coordinates from an early stage of refinement of an aconitase-isocitrate complex, we successfully predicted the binding configuration of isocitrate. Four configurations were found, the energetically most favorable of which fit the observed electron density well and was used as a starting model for further refinement. Two configurations were found in citrate docking experiments, the second of which approximates the mode of substrate binding in an aconitase-nitrocitrate complex. We were also able to propose two binding modes of the catalytic intermediate cis-aconitate. These correspond closely to the isocitrate and the citrate binding modes. The relation of these new results to the proposed reaction mechanism is discussed.
将底物自动对接至已知结构的蛋白质，可通过两种方式辅助晶体学分析过程。其一，自动对接可用于仅利用精修早期阶段的蛋白质坐标，为底物生成少量起始模型。其二，自动对接提供了一种方法，通过假设催化中间体的结合模式，来探索晶体学无法触及的催化方面。本文描述了利用自动对接来探索底物与乌头酸酶的结合。该技术从处于任意构型和位置的底物分子开始，基于分子力学类型的力场，在（静态的）蛋白质活性位点中找到有利的对接构型。利用乌头酸酶 - 异柠檬酸复合物精修早期阶段的蛋白质坐标，我们成功预测了异柠檬酸的结合构型。发现了四种构型，其中能量上最有利的构型与观察到的电子密度吻合良好，并被用作进一步精修的起始模型。在柠檬酸盐对接实验中发现了两种构型，其中第二种构型近似于乌头酸酶 - 硝基柠檬酸盐复合物中底物的结合模式。我们还能够提出催化中间体顺乌头酸的两种结合模式。这些与异柠檬酸和柠檬酸盐的结合模式密切对应。讨论了这些新结果与所提出的反应机制的关系。
