Docking of tryptophan analogs to trytophanyl-tRNA synthetase: implications for non-canonical amino acid incorporations
Docking of tryptophan analogs to trytophanyl-tRNA synthetase: implications for non-canonical amino acid incorporations
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DOI：
10.1515/bc.2008.133
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发表时间：
2008-09-01
影响因子：
3.7
通讯作者：
Budisa, Nediljko
中科院分区：
文献类型：
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作者：
Azim, M. Kamran;Budisa, Nediljko
非规范氨基酸（N-AA）作为核糖体翻译过程中肽和蛋白质的构建块，代表了几乎无限的新功能。氨酰-tRNA合成酶（阿尔斯）对氨基酸的特异性选择、活化和tRNA装载是氨酰化反应中的重要步骤。在大多数情况下，N-AA的氨酰化是相关氨基酸也将参与核糖体翻译的良好指示。然而，测试氨基酸类似物的翻译能力具有技术限制。因此，一个快速和可靠的计算机测试的N-AA识别的阿尔斯将是有利的实验设计。我们选择了来自大肠杆菌的色氨酸-tRNA合成酶作为模型系统，使用FlexX-Pharm策略与各种色氨酸类似物进行对接研究。我们能够计算TrpRS中Trp类似物的相对结合能，其与它们在E.杆菌特别地，FlexX-Pharm预测了在大肠杆菌的同源性模型中，含氟、氨基、羟基和氮杂的Trp类似物在Trp的1.5埃内的结合位点。coli TrpRS.因此，在N-AA掺入实验之前使用配体对接可能提供用于确定可有效掺入蛋白质中的N-AA的直接手段。
Non-canonical amino acids (N-AA), as building blocks for peptides and proteins during ribosomal translation, represent a nearly infinite supply of novel functions. The specific selection, activation and tRNA-charging of amino acids by aminoacyl-tRNA synthetases (AARS) in the aminoacylation reaction are essential steps. In most cases, aminoacylation of N-AA is a good indication that the related amino acid will participate in ribosomal translation as well. However, testing the translational capacity of amino acid analogs has technical limitations. Therefore, a rapid and reliable in silico test for N-AA recognition by AARS would be advantageous in experimental design. We chose tryptophanyl-tRNA synthetase from Escherichia coli as a model system for docking studies with various tryptophan analogs using the FlexX-Pharm strategy. We were able to calculate relative binding energies for Trp analogs in TrpRS that correlate well with their translational activities in E. coli. In particular, FlexX-Pharm predicted the binding sites of fluoro-, amino-, hydroxyl- and aza-containing Trp analogs within 1.5 angstrom of Trp in the homology model of E. coli TrpRS. Therefore, the use of ligand docking prior to N-AA incorporation experiments might provide a straightforward means for determining N-AA that can be efficiently incorporated into a protein.