Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan
Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan
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DOI：
10.1093/protein/gzp014
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发表时间：
2009-07-01
影响因子：
2.4
通讯作者：
Kuhara, Satoru
中科院分区：
文献类型：
--
作者：
Hirakawa, Hideki;Akita, Hidenori;Kuhara, Satoru
ALE-1是一种选择性靶向和裂解金黄色葡萄球菌的甘氨酸内肽酶，由于其对病原菌的底物特异性，有望成为下一代抗菌剂。它有一个中心催化结构域和一个叫做92AA的靶向结构域。92AA已被证明可以识别五甘氨酸，但其识别和与五甘氨酸相互作用的分子机制尚未阐明。预测五甘氨酸的结合模式对估计ALE-1的催化反应机理具有重要意义。在本研究中，我们通过计算方法表征了92AA的结合间隙，并通过结合模拟模拟了92AA与肽聚糖五甘氨酸之间形成的配合物。此外，我们进行了精确的分子动力学模拟，通过配合物识别与五甘氨酸相互作用的氨基酸残基。我们还实验构建了突变体，其中存在于结合间隙的氨基酸残基通过位点定向诱变而改变，并通过ELISA评估了它们与肽聚糖的结合能力。基于这些分析结果，我们提出了92AA与肽聚糖的五甘氨酸的结合模式，并模拟了92AA与五甘氨酸之间能量稳定的配合物。
ALE-1 is a glycylglycine endopeptidase that selectively targets and lyses Staphylococcus aureus, and is expected to be a next generation antibacterial agent because of its substrate specificity to pathogenic bacteria. It has a central catalytic domain and a targeting domain called 92AA. 92AA has been shown to recognize pentaglycine, but the molecular mechanism by which it recognizes and interacts with pentaglycine has not been elucidated. To predict the binding modes of pentaglycine is important for estimating the catalytic reaction mechanism of ALE-1. In the present study, we characterized the binding cleft of 92AA by a computational method and modeled the complexes formed between 92AA and the pentaglycine of peptidoglycan by a binding simulation. In addition, we performed precise simulations of the molecular dynamics by which the complexes identify the amino acid residues interacting with the pentaglycine. We also experimentally constructed mutants in which the amino acid residues present in the binding cleft were changed by site-directed mutagenesis and assessed their ability to bind to peptidoglycan by ELISA. Based on the results of these analyses, we proposed a mode of binding between 92AA and the pentaglycine of peptidoglycan, and modeled the energetically stable complexes between 92AA and the pentaglycine.