Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
Science. 2010 Jan 8;327(5962):202-6. doi: 10.1126/science.1181085.
Thermodynamic rules that link RNA sequences to secondary structure are well established, but the link between secondary structure and three-dimensional global conformation remains poorly understood. We constructed comprehensive three-dimensional maps depicting the orientation of A-form helices across RNA junctions in the Protein Data Bank and rationalized our findings with modeling and nuclear magnetic resonance spectroscopy. We show that the secondary structures of junctions encode readily computable topological constraints that accurately predict the three-dimensional orientation of helices across all two-way junctions. Our results suggest that RNA global conformation is largely defined by topological constraints encoded at the secondary structural level and that tertiary contacts and intermolecular interactions serve to stabilize specific conformers within the topologically allowed ensemble.
RNA 序列与其二级结构之间的热力学规则已得到充分确立，但二级结构与三维整体构象之间的联系仍知之甚少。我们构建了全面的三维图谱，描绘了蛋白质数据库中 RNA 连接点处 A 型螺旋的取向，并通过建模和核磁共振波谱学对我们的发现进行了合理化解释。我们表明，连接点的二级结构编码了易于计算的拓扑约束，这些约束能够准确预测所有双向连接点处螺旋的三维取向。我们的研究结果表明，RNA 的整体构象主要由二级结构水平上编码的拓扑约束所决定，而三级结构接触和分子间相互作用则有助于在拓扑允许的范围内稳定特定构象。
