Abstract

In present work, we describe a methodology for prediction of an enzymatic reaction for which no experimental data are available except for a gene sequence. As a challenging case, we have developed the method for identifying the putative substrates of monoester phosphatases, commonly known as acid phosphatase enzymes, which have no strong substrate specificity. Finding a preferable substrate for each one is an important task to unravel pathways involved in plant phosphate metabolism. Having used an Arabidopsis thaliana haloacid dehalogenase (HAD)-related acid phosphatases, HRP9, with an experimentally known structure and preferred substrate as an instance, we firstly predicted the 3 D-structure of HRP1 for subsequent analysis. Then, molecular docking was used to find the best protein interaction with a ligand existing in a set of possible substrates compiled from genome scale metabolic networks of A. thaliana based on binding energy, binding mode as well as the distance between phosphoric ester and cofactor, Mg²⁺, localized in the active site of HRP1. Molecular dynamics simulation ratified stable protein-ligand complex model. Our analysis predicted HRP1 preferably bind to pyridoxamine-5′-phosphate (PMP). Thus, it is deduced that the conversion of PMP to pyridoxamine must be catalyzed by HRP1. This procedure is expected to make a reliable pipeline to predict the enzymatic reactions catalyzed by acid phosphatases. Taken as a whole, it could be applicable for discovery of the interacting ligands, inhibitors as well as interacting proteins which limits lab works or used for gap filling in biosystems.

Communicated by Ramaswamy H. Sarma

摘要

在目前的工作中，我们描述了一种预测酶促反应的方法，除了基因序列外，没有可用的实验数据。作为一个具有挑战性的案例，我们开发了识别单酯磷酸酶的假定底物的方法，通常称为酸性磷酸酶，它没有很强的底物特异性。为每一种寻找合适的底物是解开植物磷酸盐代谢途径的一项重要任务。使用拟南芥卤酸脱卤酶 (HAD) 相关酸性磷酸酶 HRP9 具有实验上已知的结构和优选底物作为实例，我们首先预测了 HRP1 的 3D 结构用于后续分析。然后，基于结合能、结合模式以及磷酸酯和辅因子之间的距离，分子对接用于寻找与拟南芥基因组规模代谢网络编译的一组可能底物中存在的配体的最佳蛋白质相互作用，镁²⁺，定位于 HRP1 的活性位点。分子动力学模拟证实了稳定的蛋白质-配体复合物模型。我们的分析预测 HRP1 最好与 5'-磷酸吡哆胺 (PMP) 结合。因此，推断 PMP 向吡哆胺的转化必须由 HRP1 催化。该程序有望成为预测酸性磷酸酶催化的酶促反应的可靠管道。总的来说，它可以用于发现相互作用的配体、抑制剂以及相互作用的蛋白质，这些蛋白质限制了实验室工作或用于生物系统中的间隙填充。

由 Ramaswamy H. Sarma 交流