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首页> 外文期刊>Journal of Molecular Biology >Molecular dynamics simulation reveals conformational switching ofwater-mediated uracil-cytosine base-pairs in an RNA duplex
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Molecular dynamics simulation reveals conformational switching ofwater-mediated uracil-cytosine base-pairs in an RNA duplex

机译：分子动力学模拟揭示RNA双链体中水介导的尿嘧啶胞嘧啶碱基对的构象转换

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摘要

A 4 ns molecular dynamics simulation of an RNA duplex (r-GGACUUCGGUCC)(2) in solution with Na+ and Cl- as counterions was performed. The X-ray structure of this duplex includes two water-mediated uracil-cytosine pairs. In contrast to the other base-pairs in the duplex the water-mediated pairs switch between different conformations. One conformation corresponds to the geometry of the water-mediated UC pairs in the duplex X-ray structure with water acting both as hydrogen-bond donor and acceptor. Another conformation is close to that of a water-mediated UC base-pair found in the X-ray structure of the 23 S rRNA sarcin/ricin domain. Ln this case the oxygen of the water molecule is linked to two-base donor sites. For a very short time also a direct UC base-pair and a further conformation that is similar to the one found in the RNA duplex structure but exhibits an increased H3(U)...N3(C) distance is observed. Water molecules with unusually long residence times are involved in the water-mediated conformations. These results indicate that the dynamic behaviour of the water-mediated UC base-pairs differs from that of the duplex Watson-Crick and non-canonical guanine-uracil pairs with two or three direct hydrogen bonds. The conformational variability and increased flexibility has to be taken into account when considering these base-pairs as RNA building blocks and as recognition motifs.
机译：进行了以Na +和Cl-为抗衡离子的溶液中RNA双链体（r-GGACUUCGGUCC）（2）的4 ns分子动力学模拟。该双链体的X射线结构包括两个水介导的尿嘧啶-胞嘧啶对。与双链体中的其他碱基对相反，水介导的对在不同构象之间切换。一种构型对应于双链X射线结构中水介导的UC对的几何结构，其中水同时充当氢键供体和受体。另一个构象与在23 S rRNA sarcin / ricin域的X射线结构中发现的水介导UC碱基对的构象接近。在这种情况下，水分子的氧与两个碱基的供体位点相连。在很短的时间内，还可以观察到直接的UC碱基对和类似于RNA双链体结构但呈现出增加的H3（U）... N3（C）距离的进一步构象。具有异常长的停留时间的水分子参与水介导的构象。这些结果表明，水介导的UC碱基对的动力学行为不同于具有两个或三个直接氢键的双链沃森-克里克和非经典鸟嘌呤-尿嘧啶对的动力学行为。当将这些碱基对视为RNA构件和识别基元时，必须考虑构象变异性和增加的灵活性。

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