Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site
Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site
复制标题
DOI：
10.1021/ja0741933
复制
发表时间：
2008-01-30
影响因子：
15
通讯作者：
Simonson, Thomas
中科院分区：
文献类型：
--
作者：
Aleksandrov, Alexey;Simonson, Thomas
四环素类(TC)是抑制细菌核糖体的重要抗生素。在Thermus thermophilus 30S核糖体亚基的两个X射线结构中，分别发现了两个和六个Tc结合位点；各种位点的确切功能作用尚不清楚。我们研究了两个共同的位点，在两种结构中都可以看到：一个初级位点，它被定位为阻止tRNA A-位点结合，另一个次要位点，它具有较弱的电子密度。我们结合分子动力学模拟和连续体静电计算来估计两个位置的相对亲和力。核糖体的介电常数被设置为8，以再现TC与其类似物米诺环素和多西环素之间的实验结合自由能差异，以及更严格的镁离子结合自由能模拟。我们发现，这两个位置都包括一个预结合的镁离子，在TC结合之前就存在。通过长时间的模拟和比较每个中心的8个结构模型，我们发现初级中心的结合强度要强1-4千卡/摩尔；这一范围似乎与两个中心的结晶学观察到的占有率相一致。在这个自由能范围内，TET5在生理条件下基本上是空闲的。因此，我们认为主要部位是抑制部位，变构效应可能不是四环素功能所必需的。
Tetracyclines (Tc) are important antibiotics that inhibit bacterial ribosomes. Two and six Tc binding sites, respectively, were seen in two X-ray structures of the Thermus thermophilus 30S ribosome subunit; the exact functional role of the various sites remains unclear. We study the two consensus sites, seen in both structures: a primary site, which is positioned to block tRNA A-site binding, and a secondary site, which has a weaker electron density. We combine molecular dynamics simulations and continuum electrostatic calculations to estimate the relative affinities of the two sites. The dielectric constant of the ribosome is set to 8, to reproduce the experimental binding free energy differences between Tc and its analogues minocycline and doxycycline, as well as more rigorous free energy simulations of Mg2+ binding. We find that both sites include a prebound Mg2+ ion, present before Tc binds. Using long simulations and comparing eight structural models for each site, we then show that primary site Tc binding is stronger by 1-4 kcal/mol; this range appears consistent with the crystallographically observed occupancies of the two sites. With this free energy range, TET5 is largely unoccupied under physiological conditions. Thus, we propose that the primary site is the inhibitory site and that allosteric effects may not be essential for tetracycline function.