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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes
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Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes

机译：卟啉与两个反平行的人端粒四链体相互作用的分子动力学研究

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摘要

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.
机译：我们通过分子动力学模拟研究了卟啉衍生物（TMPyP4）与两个反平行篮子型人类端粒四链体在钾离子条件下的结合相互作用。为每个四链体构建了九个四链体-化学计量比为1：1的TMPyP4复合体，包括末端堆叠，插层，外部凹槽结合和外部环堆叠的结合模式。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，末端堆积模式是最佳的结合模式，具有高结合亲和力和高稳定性的四重体，其次是外部环堆积方式，具有较高的结合亲和力和高稳定性的四重体。凹槽结合模式具有相对较低的结合亲和力，并且四链体稳定良好。插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出非常高的柔韧性。

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