Solution structure of an informationally complex high-affinity RNA aptamer to GTP
Solution structure of an informationally complex high-affinity RNA aptamer to GTP
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DOI：
10.1261/rna.2251306
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发表时间：
2006-04-01
期刊：
影响因子：
4.5
通讯作者：
Szostak, JW
中科院分区：
文献类型：
--
作者：
Carothers, JM;Davis, JH;Szostak, JW
GTP的高亲和力RNA适体比低亲和力适体在信息上更复杂。类似物结合研究表明，提高亲和力所需的额外信息并不能说明与配体的更多相互作用。根据这些观察结果，我们希望了解使复杂适体能够以更高亲和力结合其配体的结构特征。在这里，我们提出了41-nt的I类GTP适体（Kd = 75 nM）的溶液结构，通过NMR测定。适体的骨架形成结合口袋的反S。配体核碱基堆叠在嘌呤平台之间，并与另一个碱基的边缘形成氢键。有趣的是，I类适体和结合ATP的RNA适体的局部相互作用模式非常相似，K（d）为6 μ M。适体表现出几乎相同水平的结合特异性和从溶剂中螯合的配体分数（81% - 85%）。然而，GTP适体在信息上更复杂（类似于45位对35位），并且具有更大的识别凸起（15个对12个核苷酸），具有更多稳定的碱基-碱基相互作用。由于适体具有相似的配体结合模式，我们得出结论，I类适体中的稳定结构元件是造成Kd差异的主要原因。这些结果与以下假设一致：增加RNA内相互作用的数量，而不是增加与配体的特异性接触，是提高结合亲和力的最简单方法。
Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K-d = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K(d)of 6 mu M are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81% - 85%). However, the GTP aptamer is more informationally complex (similar to 45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base - base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in Kd. These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.