物理化学学报 >> 2010, Vol. 26 >> Issue (02): 478-486.doi: 10.3866/PKU.WHXB20100219

生物物理化学 上一篇    下一篇

鸟嘌呤四链体中Na+的移动

郭慈, 刘翠, 杨忠志   

  1. 辽宁师范大学化学化工学院, 辽宁 大连 116029
  • 收稿日期:2009-09-11 修回日期:2009-11-20 发布日期:2010-01-26
  • 通讯作者: 杨忠志 E-mail:zzyang@lnnu.edu.cn

Mobility of Na+ in a G-Quadruplex

GUO Ci, LIU Cui, YANG Zhong-Zhi   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
  • Received:2009-09-11 Revised:2009-11-20 Published:2010-01-26
  • Contact: YANG Zhong-Zhi E-mail:zzyang@lnnu.edu.cn

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摘要：

Na+-G-四链体复合物是一个明显的极化体系, 其形成或解离过程中, Na+的移动路线目前还不十分明确. σπ水平的原子-键电负性均衡方法融合进分子力学(ABEEMσπ/MM)模型除原子位点外, 还明确地定义了孤对电子、σ键和π键的位置, 并且各位点电荷随分子环境改变而浮动, 因此能更好地反映该体系的极化现象. 本文应用ABEEMσπ/MM方法研究了Na+-G-四平面复合物的性质, 包括它的几何构型、电荷分布和结合能等, 并在MP2/6-31G(d,p)水平上做了相应的从头算, 两种结果十分吻合. Na+的存在改变了G-tetrad的氢键方式. 通过比较Na+各条移动路线中体系的结合能, 预测G-四链体中三个Na+最有可能沿α方向依次移出. 以上研究为进一步应用ABEEMσπ/MM模型进行G-四链体中离子交换通道的动力学模拟打下坚实的基础.

关键词: G-四链体, Na+-G-四平面, ABEEMσπ/MM方法, 从头算, 移动路线

Abstract:

The Na+-G-quadruplex complex is a polarized system and the mobility of Na+ during its formation or decomposition is still unclear. The atombond electronegativity equalization method at the σπ level fused into molecular mechanics (ABEEMσπ/MM) model clearly defines the lone-pair electron, σ bond and π bond sites in addition to the atomic sites. The partial charge fluctuation is calculated in accordance with a change in the molecular environment and so this method should account well for the polarization effect. In this paper, we discuss some properties for the Na+-G-tetrad complex including its geometry, charge distribution, and binding energy according to the ABEEMσπ/MM method. We also investigate these properties for the Na+-G-tetrad complex using the ab initio method at the MP2/6-31G(d,p) level. The ABEEMσπ/MM results are in good agreement with the ab initio results. The presence of Na+ changes the hydrogen bonds in the G-tetrad. By comparing the binding energy of the systemfor every Na+ mobile path, we predict that the most probable path is that three Na+ ions move away individually from the G-quadruplex along the α orientation. This study lays a solid foundation for the dynamic simulation of ion exchange channels in a G-quadruplex using the ABEEMσπ/MM model.

Key words: G-quadruplex, Na+-G-tetrad, ABEEMσπ/MM method, Ab initio, Mobile path