Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes
Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes
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卟啉与两个反向平行人端粒四链体相互作用的分子动力学研究
DOI：
10.1021/jp101373p
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发表时间：
2010-05-13
影响因子：
3.3
通讯作者：
Li, Ze-Sheng
中科院分区：
文献类型：
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作者：
Li, Ming-Hui;Luo, Quan;Li, Ze-Sheng
采用分子动力学模拟方法研究了卟啉衍生物TMPyP 4与两个反平行篮状端粒四链体在K+离子条件下的相互作用。每个四链体构建了9个四链体TMPyP 4复合物，每个复合物具有1：1的化学计量比，包括末端堆积、插入、外部沟结合和外部环堆积的结合模式。进行了详细的结构分析、自由能计算和主成分分析。结果表明，末端堆积方式结合效果最好，结合亲和力高，四链体稳定性高;其次是外环堆积方式，结合亲和力相对较高，四链体稳定性高。沟槽结合模式具有较低的结合亲和力，四链体稳定性较好。嵌入模式具有非常高的结合亲和力，但是四链体不稳定并且显示非常高的柔性。
We investigated the binding interactions of a porphyrin derivative (TMPyP4) with two antiparallel basket-type human telomeric quadruplexes under K+ ion conditions by molecular dynamics simulations. Nine quadruplex TMPyP4 complexes each with a 1:1 stoichiometry were built for every quadruplex, including the binding modes of end stacking, intercalation, external groove binding, and external loop stacking. Detailed structures analysis, free energy calculations, and principal components analysis were performed. The results show that the end stacking mode is the best binding mode, with high binding affinity and high stability of quadruplexes, and next is the external loop stacking mode, with relatively high binding affinity and high stability of quadruplexes. The groove binding mode has the relatively low binding affinity, and the quadruplexes are stabilized well. The intercalation mode has very high binding affinity, but the quadruplexes are not stabilized and show very high flexibility.