物理化学学报 >> 2009, Vol. 25 >> Issue (04): 783-791.doi: 10.3866/PKU.WHXB200904241

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人体端粒中(3+1)混合结构G-四链体稳定性的分子动力学模拟

沈新媛 吕洋 李慎敏   

  1. 大连大学, 辽宁省生物有机化学重点实验室, 辽宁 大连 116622
  • 收稿日期:2008-11-04 修回日期:2008-12-11 发布日期:2009-03-31
  • 通讯作者: 李慎敏 E-mail:shenmin@dl.cn

Molecular Dynamics Simulations on the Stability of (3+1) Mixed-Type Hybrid G-quadruplex in Human Telomere

 CHEN Xin-Yuan, LV Yang, LI Shen-Min   

  1. Liaoning Key Laboratory of Bioorganic Chemistry, Dalian University, Dalian 116622, Liaoning Province, P. R. China
  • Received:2008-11-04 Revised:2008-12-11 Published:2009-03-31
  • Contact: LI Shen-Min E-mail:shenmin@dl.cn

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摘要： 利用分子动力学模拟方法, 考察了人体端粒中(3+1)混合结构G-四链体的结构及稳定性问题. 讨论了配位K+离子、药物分子(端粒抑素)和溶剂水分子对G-四链体的Hoogsteen氢键结构、π-π堆积作用的影响. 研究表明, K+离子与鸟嘌呤碱基上O6原子的配位作用减弱了对角鸟嘌呤间O6-O6的静电排斥作用, 使得相邻的四个鸟嘌呤能够以Hoogsteen氢键结合的方式形成具有近平面结构的稳定G-四平面. 另一方面, G-四平面间、G-四平面与药物分子间的π-π堆积作用降低了G-四链体复合物的总能, 有利于其稳定存在. 此外, 溶剂水分子主要分布在G-四链体的TTA环、骨架和糖环的周围, 使其位移涨落增大; 然而, 在3 ns动力学模拟中, 由于水分子没有进入到G-四链体的空腔中, 溶剂水对G-四平面的结构影响不明显.

关键词: G-四链体, G-四平面, Hoogsteen 氢键, π-π堆积作用, 分子动力学模拟, 端粒抑素

Abstract: We used molecular dynamics simulations to investigate the structure and stability of a mixed-type hybrid guanine-quadruplex complex in human telomere. The effects of coordinated K+ ions, drug ligands (TMS) and solvent molecules on stability are discussed. Our results show that coordination between K+ ions and O6 in guanine bases decreases the electrostatic repulsion of the diagonal O6-O6. As a result, planar G-tetrads are stabilized by Hoogsteen hydrogen bonds that are formed by four neighboring guanine bases. On the other hand, stacking interactions between G-tetrads as well as the G-tetrad and the drug ligand lower the total energy of the G-quadruplex complex and thus stabilize it. In addition, water molecules are mainly located around TTA loops, the backbone and sugar rings which result in larger root mean square deviations (RMSDs) compared with other G-quadruplex fragments. However, since water does not enter the G-quadruplex complex cages during the 3 ns simulation, the influence of solvent on the stability of the G-tetrads is insignificant.

Key words: G-quadruplex, G-tetrad, Hoogsteen hydrogen bond, π-&pi, stacking interaction, Molecular dynamics simulation, Telomestatin