Effects of monohydration on an adenine-thymine base pair
Effects of monohydration on an adenine-thymine base pair
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一水合对腺嘌呤-胸腺嘧啶碱基对的影响
DOI：
10.1007/s00214-015-1686-7
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
and M. Tachikawa
中科院分区：
文献类型：
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作者：
S. Watanabe;Y. Ogata;T. Kawatsu;Y. Kawashima;and M. Tachikawa
我们使用包括核量子和热效应的路径积分分子动力学模拟分析了腺嘌呤-胸腺嘧啶碱基对之间的氢键结构的单水合效应。我们专注于两个单水合模型的腺嘌呤-胸腺嘧啶碱基对与水分子绑定到每个腺嘌呤和胸腺嘧啶网站。还讨论了没有水分子的腺嘌呤-胸腺嘧啶碱基对，以揭示水分子在单水合模型中的作用。我们发现，单水合作用的变化取决于水分子的位置。单水合作用对分子间运动的影响也采用主成分分析进行了研究。单水合作用改变了腺嘌呤-胸腺嘧啶碱基对的分子间运动。我们发现，核量子效应对运动的影响依赖于束缚水分子的位置。核量子效应对腺嘌呤、胸腺嘧啶和水分子的氢键结构影响很小，但对一水合碱基对体系的分子间运动却有很大的影响。
We analyzed the monohydration effect on the hydrogen-bonded structure between the adenine–thymine base pair using path integral molecular dynamics simulations including the nuclear quantum and thermal effects. We focused on two monohydration models for an adenine–thymine base pair with a water molecule bound to each adenine and thymine site. The adenine–thymine base pair without a water molecule was also discussed to reveal the role of a water molecule in monohydrated models. We found that the monohydration effect varies depending on the location of the water molecule. The monohydration effect on the inter-molecular motions is also investigated using the principle component analysis. The monohydration alters the inter-molecular motions of adenine–thymine base pair. We found that the nuclear quantum effect on the motion depends on the positions of the bound water molecule. The nuclear quantum effect on the hydrogen-bonded structure of adenine, thymine and water molecules is rather small, but we found significantly large nuclear quantum effect on the inter-molecular motions of the monohydrated base pair systems.