Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures
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DOI：
10.1186/1472-6807-11-41
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发表时间：
2011-10-19
影响因子：
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通讯作者：
Carugo, Oliviero
中科院分区：
文献类型：
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作者：
Kirillova, Svetlana;Carugo, Oliviero
背景：水合作用对RNA的结构和功能至关重要。X射线结晶学是确定RNA结构和水合作用的最常用方法，因此，统计调查是基于结晶学结果，而结晶学结果的数量正在迅速增加。结果：对未配对的RNA核苷酸高分辨X射线结构中水分子分布的统计分析表明：不同碱基具有相同的被水分子包围的倾向；水分子簇指示可能的水化位点，在某些情况下，与RNA和DNA双螺旋的主槽和小槽相匹配；复杂的氢键网络表征了核苷酸的溶剂化，导致碱基及其周围水分子的显著刚性。有趣的是，一般情况下，未配对的RNA碱基周围的水合位置与形成碱基对时第二个核苷酸所占据的位置不匹配。它们不复制Watson-Crick对中互补碱基的原子位置。
Background: Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing.Results: A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed.Conclusions: The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.