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Hydration of protein-RNA recognition sites

机译：蛋白质-RNA识别位点的水合

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摘要

We investigate the role of water molecules in 89 protein-RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein-RNA interfaces are hydrated less than protein-DNA interfaces, but more than protein-protein interfaces. Majority of the waters at protein-RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively 'dry' than interfaces with tRNA and duplex RNA. In contrast to protein-DNA interfaces, mainly due to the presence of the 2'OH, the ribose in protein-RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein-RNA interfaces is hydrated more than the major groove, while in protein-DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein-RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein-RNA recognition and should be carefully treated while engineering protein-RNA interfaces.
机译：我们调查了水分子在从蛋白质数据库中提取的89种蛋白质-RNA复合物中的作用。与双链或核糖体蛋白相比，具有tRNA和单链RNA的水分较少。蛋白质-RNA界面的水合性小于蛋白质-DNA界面，但大于蛋白质-蛋白质的界面。蛋白质-RNA界面处的大部分水都形成多个H键;但是，一小部分什么也没做。那些形成氢键的人比其伴侣蛋白更偏爱RNA的极性基团。水的空间分布使得与核糖体蛋白和单链RNA的界面比与tRNA和双链RNA的界面相对“干燥”。与蛋白质-DNA界面相反，主要是由于2'OH的存在，蛋白质-RNA界面中的核糖比磷酸盐或碱的水合程度更高。蛋白质-RNA界面中的次要凹槽比主要凹槽中的水分更多，而蛋白质-DNA界面中的次要凹槽则相反。这些链在单位界面区域中形成最多数量的水介导的H键，其次是螺旋和非规则结构。蛋白质-RNA界面处保存的水比其他水具有更多的氢键。保留的水有助于蛋白质-RNA识别中的亲和力，在工程化蛋白质-RNA界面时应小心处理。

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