Aminoglycoside antibiotics: A-site specific binding to 16S
Aminoglycoside antibiotics: A-site specific binding to 16S
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DOI：
10.1016/j.ijms.2009.02.010
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发表时间：
2009-06-01
影响因子：
1.8
通讯作者：
Bowers, Michael T.
中科院分区：
文献类型：
--
作者：
Baker, Erin Shammel;Dupuis, Nicholas F.;Bowers, Michael T.
16 S rRNA的A位点是已知的氨基糖苷类结合位点，其是参与原核翻译的30 S核糖体亚基的一部分。氨基糖苷类药物结合后A位点的构象变化的完整表征对于未来RNA/药物复合物的开发至关重要;然而，16 S的重复性使得这非常困难。最近，研究发现，包含16 S的A位点亚结构域的27个碱基的RNA构建体（16 S（27））的行为与整个A位点结构域相似。本研究利用电喷雾质谱、离子迁移率和分子动力学方法分析了核糖霉素（R）、巴龙霉素（P）和利维多霉素（L）加入前后16 S（27）的A位。单独16 S（27）的ESI质谱图显示了单链16 S（27）和双链（16 S（27））（2）复合物。加入氨基糖苷类后，质谱显示只有一种氨基糖苷类与16 S结合（27），而一种或两种氨基糖苷类与（16 S（27））结合（2）。利用离子迁移率测量和分子动力学计算确定了16 S（27）和（16 S（27））（2）配合物的无溶剂结构。这些研究发现16 S（27）以发夹构象存在，而（16 S（27））（2）以十字形存在。只有一个氨基糖苷类与16 S（27）发夹的单个A位点结合，这种连接会压缩发夹。由于（16 S（27））（2）十字形存在两个A位点，因此可以结合一种或两种氨基糖苷类。氨基糖苷类压缩A位点，导致仅结合一个氨基糖苷类的十字形大于结合两个氨基糖苷类的十字形。在任何氨基糖苷类/16 S（27）复合物中均未观察到非特异性结合。(C)2009爱思唯尔有限公司版权所有。
The A-site of 16S rRNA, which is a part of the 30S ribosomal subunit involved in prokaryotic translation, is a well known aminoglycoside binding site. Full characterization of the conformational changes undergone at the A-site upon aminoglycoside binding is essential for development of future RNA/drug complexes; however, the massiveness of 16S makes this very difficult. Recently, studies have found that a 27 base RNA construct (16S(27)) that comprises the A-site subdomain of 16S behaves similarly to the whole A-site domain. ESI-MS, ion mobility and molecular dynamics methods were utilized in this study to analyze the A-site of 16S(27) before and after the addition of ribostamycin (R), paromomycin (P) and lividomycin (L). The ESI mass spectrum for 16S(27) alone illustrated both single-stranded 16S(27) and double-stranded (16S(27))(2) complexes. Upon aminoglycoside addition, the mass spectra showed that only one aminoglycoside binds to 16S(27), while either one or two bind to (16S(27))(2). Ion mobility measurements and molecular dynamics calculations were utilized in determining the solvent-free structures of the 16S(27) and (16S(27))(2) complexes. These studies found 16S(27) in a hairpin conformation while (16S(27))(2) existed as a cruciform. Only one aminoglycoside binds to the single A-site of the 16S(27) hairpin and this attachment compresses the hairpin. Since two A-sites exist for the (16S(27))(2) cruciform, either one or two aminoglycosides may bind. The aminoglycosides compress the A-sites causing the cruciform with just one aminoglycoside bound to be larger than the cruciform with two bound. Non-specific binding was not observed in any of the aminoglycoside/16S(27) complexes. (C) 2009 Elsevier B.V. All rights reserved.