高等学校化学学报

高等学校化学学报

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Tobramycin与16S rRNA A位点复合物的分子动力学模拟

冯宇1, 张旭东1, 程伟贤1, 曹槐1, 刘次全1,2   

    1. 云南大学现代生物学研究中心, 昆明 650091;
    2. 中国科学院昆明动物研究所, 昆明 650223
  • 收稿日期:2007-02-27 修回日期:1900-01-01 出版日期:2007-11-10 发布日期:2007-11-10
  • 通讯作者: 刘次全

Molecular Dynamics Simulation on the Complex of the Tobramycin and 16S rRNA A Site

FENG Yu1, ZHANG Xu-Dong1, CHENG Wei-Xian1,CAO Huai1, LIU Ci-Quan1,2*   

    1. Modern Biological Research Center, Yunnan University, Kunming 650091, China;
    2. Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  • Received:2007-02-27 Revised:1900-01-01 Online:2007-11-10 Published:2007-11-10
  • Contact: LIU Ci-Quan

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摘要： 采用分子动力学方法(Molecular dynamics, MD)对托普霉素(Tobramycin)与16S rRNA的A位点复合物的特异性识别机制进行了理论模拟研究, 模拟时间为3.6 ns. 结果表明, A位点中波动最大的部位是两个环外碱基A1492和A1493; tobramycin的环Ⅰ和环Ⅱ是其最保守的结构单元, 可能参与了Tobramycin与16S rRNA的A位点之间的特异性识别. 另外, 发现一个残存时间为3.6 ns的“结构化”水分子, 它桥接了Tobramycin环Ⅱ的N3与环Ⅰ的N6'之间的氢键, 稳定了Tobramycin的结构; Tobramycin周围水合密度较高的位点出现在环Ⅰ和环Ⅱ附近, 这也正是晶体结构中形成较多水媒介氢键及动力学模拟中结构化水分子出现的位置. 动力学模拟证实Tobramycin与16S rRNA间的结合是大量氢键及水分子相互作用的结果, 这有助于设计和开发以Tobramycin为基础, 具有高亲和力及特异性的16S rRNA抑制剂.

关键词: 分子动力学, 托普霉素, 16S rRNA A 位点, 水合密度

Abstract: A 3.6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two looped out bases(A1492 and A1493) of the A site is the flexible part, while ringⅠand ringⅡ of tobramycin are the most conservative elements. Moreover, ringⅠand ringⅡ of tobramycin may be function conservative unit which may participate in the specificity recognition for tobramycin binding to the 16S rRNA A site. In addition, a structural water molecule was detected during the whole MD simulation trajectory, which bridged the contacts between ringⅡ(N3)and ringⅠ(N6') of tobramycin and enhanced the rigid of tobramycin structure. There is one hydration site with the higher water density in the vicinity of ringⅠand ringⅡ of tobramycin. This result is consistent with the crystal structure detected that the most water-medial hydrogen bonds were listed in the same situation. Our study illustrates that recognition mechanism between tobramycin and 16S rRNA A site was due to a few hydrogen bond and water molecule interactions, which play a great role in designing high affinity and speciality inhibitors of 16S rRNA A site based on tobramycin.

Key words: Molecular dynamics, Tobramycin, 16S rRNA A site, Hydration density

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