Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.
Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.
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DOI：
10.1093/nar/gkr1154
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发表时间：
2012-04
影响因子：
14.9
通讯作者：
Dayie TK
中科院分区：
文献类型：
--
作者：
Chen B;Zuo X;Wang YX;Dayie TK
核糖开关是一个新发现的结构化功能RNA元件大家族，其特异性结合无数细胞代谢产物中的小分子靶点以调节基因表达。通过X射线晶体学和核磁共振（NMR）光谱学对配体结合的核糖开关的结构研究提供了对详细的RNA-配体识别和相互作用的深入了解。然而，无配体的核糖开关的结构仍然很差的特点。在这项研究中，我们使用了各种生物化学，生物物理和计算技术，包括小角X射线散射和NMR光谱来表征配体的自由和配体结合形式的SAM-II核糖开关。我们的数据表明，RNA采用多个构象沿着其折叠途径，并表明，RNA经历了显着的构象变化后，Mg 2+压缩和S-腺苷甲硫氨酸（SAM）代谢产物结合。进一步的研究表明，Mg 2+离子对配体结合不是必需的，但可以通过促进环/茎相互作用来稳定复合物。当Mg ~（2+）离子浓度达到毫摩尔浓度时，RNA样品的构象更加紧密.这种构象接近但不同于天然折叠，并能够结合代谢物。我们的结论是，各种二级和三级结构元素，包括一个假结的形成，发生隔离后代谢物结合的RNA的假定的Shine-Dalgarno序列。
Riboswitches are a newly discovered large family of structured functional RNA elements that specifically bind small molecule targets out of a myriad of cellular metabolites to modulate gene expression. Structural studies of ligand-bound riboswitches by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy have provided insights into detailed RNA–ligand recognition and interactions. However, the structures of ligand-free riboswitches remain poorly characterized. In this study, we have used a variety of biochemical, biophysical and computational techniques including small-angle X-ray scattering and NMR spectroscopy to characterize the ligand-free and ligand-bound forms of SAM-II riboswitch. Our data demonstrate that the RNA adopts multiple conformations along its folding pathway and suggest that the RNA undergoes marked conformational changes upon Mg2+ compaction and S-adenosylmethionine (SAM) metabolite binding. Further studies indicated that Mg2+ ion is not essential for the ligand binding but can stabilize the complex by facilitating loop/stem interactions. In the presence of millimolar concentration of Mg2+ ion, the RNA samples a more compact conformation. This conformation is near to, but distinct from, the native fold and competent to bind the metabolite. We conclude that the formation of various secondary and tertiary structural elements, including a pseudoknot, occur to sequester the putative Shine–Dalgarno sequence of the RNA only after metabolite binding.
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影响因子：
14.9
作者：
Kelley JM;Hamelberg D
通讯作者：
Hamelberg D
解决 RNA 结构生物学中重大问题的关键标记技术。
影响因子：
5.6
作者：
Dayie KT
通讯作者：
Dayie KT
影响因子：
6.1
作者：
Kozin, MB;Svergun, DI
通讯作者：
Svergun, DI
影响因子：
64.8
作者：
Batey, RT;Gilbert, SD;Montange, RK
通讯作者：
Montange, RK
影响因子：
14.8
作者：
Haller, Andrea;Rieder, Ulrike;Micura, Ronald
通讯作者：
Micura, Ronald