Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
J Phys Chem B. 2011 Dec 1;115(47):13897-910. doi: 10.1021/jp2065584. Epub 2011 Nov 7.
The RNA kink-turn is an important recurrent RNA motif, an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A•G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G═C receptor base pair during evolution while the inverted pair (C═G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G═C and C═G base pairs in sequences. We carried out an extended set (~5 μs) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with ~0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. The trends seen in the simulations reveal that the A-I/G═C arrangement is preferred over all three other structures. The A-I/C═G triple appears structurally entirely unstable, consistent with the covariation patterns seen during the evolution. The A-0 arrangements tend to shift toward the A-I pattern in simulations, which suggests that formation of the A-0 interaction is likely supported by the surrounding protein and RNA molecules. A-0 may also be stabilized by additional kink-turn nucleotides not belonging to the kink-turn consensus, as shown for the kink-turn from ribosomal Helix 15. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G═C and A-I/C═G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.
RNA 扭结是一种重要的反复出现的 RNA 基序，是一种具有特征性保守三维结构的内部环。RNA 扭结的功能排列显示出磷酸二酯骨架的急剧弯曲。在其他特征相互作用中，扭结在它们的两个茎之间形成 A- 小沟 I（A-I）相互作用。大多数扭结具有扩展的 A- 小沟 I（A-I）相互作用，其中 NC 茎的第二个 A•G 碱基对的腺嘌呤通过跨糖边缘/糖边缘（tSS）和顺糖边缘/糖边缘（cSS）相互作用与 C 茎的第一个规范碱基对（即受体对）相互作用。其余的扭结具有不太紧凑的 A- 小沟 0（A-0）相互作用，只有一个 tSS 接触。我们表明，在核糖体 X 射线结构中具有 A-I 的扭结在进化过程中保持 G═C 受体碱基对，而相反的碱基对（C═G）则没有实现。相比之下，在观察到的结构中具有 A-0 的扭结在序列中交替出现 G═C 和 C═G 碱基对。我们进行了一组扩展的（~5 μs）扭结的显式溶剂分子动力学模拟，以合理化这种结构/进化模式。模拟使用净中性 Na(+)阳离子气氛（阳离子浓度约为 0.25 M）进行，并用过量盐 KCl 气氛或包含 Mg(2+)的模拟进行补充。结果似乎不依赖于离子的处理。模拟从几个扭结的 X 射线结构开始，同时我们测试了模拟系统对碱基取代、适度结构扰动和约束的响应。模拟中看到的趋势表明，A-I/G═C 排列优于所有其他三种结构。A-I/C═G 三螺旋在结构上完全不稳定，与进化过程中观察到的协变模式一致。A-0 排列在模拟中倾向于向 A-I 模式转变，这表明 A-0 相互作用的形成可能得到周围蛋白质和 RNA 分子的支持。A-0 也可能通过不属于扭结共识的额外扭结核苷酸得到稳定，如核糖体螺旋 15 的扭结所示。对所有四个 A- 小沟三螺旋的量子化学计算表明，在 A-I/G═C 和 A-I/C═G 三螺旋中，静电和色散稳定的平衡不同，这可能解释了这些在扭结背景下具有相同结构的三螺旋的不同行为。
