Importance of partially unfolded conformations for Mg2+-lnduced folding of RNA tertiary structure:: Structural models and free energies of Mg2+ interactions
Importance of partially unfolded conformations for Mg2+-lnduced folding of RNA tertiary structure:: Structural models and free energies of Mg2+ interactions
复制标题
DOI：
10.1021/bi062284r
复制
发表时间：
2007-09-11
期刊：
影响因子：
2.9
通讯作者：
Draper, David E.
中科院分区：
文献类型：
--
作者：
Grilley, Dan;Misra, Vinod;Draper, David E.
在单价盐溶液中的RNA分子通常采用一组仅包含二级结构、中间体或I状态的部分折叠构象。Mg 2+的加入强烈地稳定了相对于I状态的天然三级结构（N状态）。在本文中，结合实验和计算的方法来估计的自由能的Mg 2+与部分折叠的I状态RNA的相互作用，并考虑的可能性，Mg 2+有利于“压缩”的I状态的构象具有较高的平均电荷密度。一个序列的变体与一个显着不稳定的三级结构被用作模拟的I状态RNA，通过小角X-射线散射测量，它采用了一个渐进的更紧凑的构象在一个广泛的Mg 2+浓度范围。用荧光滴定法测定了Mg ~（2+）与I态模拟物相互作用的平均自由能。为了进一步解释这些实验数据，我们生成了I态的分子模型，并将其用于非线性Poisson-Boltzmarm方程的计算中，以估计随着平均I态尺寸从膨胀减小到紧凑，Mg 2 +-RNA相互作用自由能的变化。同样的模型也被用来定量再现实验的差异，过量Mg 2+之间的N和I状态。在这些实验和计算的基础上，I态压缩似乎将Mg 2 +-I态相互作用自由能提高10- 20%，但这种提高至多是该rRNA片段的总体Mg 2+相关稳定自由能的5%。
RNA molecules in monovalent salt solutions generally adopt a set of partially folded conformations containing only secondary structure, the intermediate or I state. Addition of Mg2+ strongly stabilizes the native tertiary structure (N state) relative to the I state. In this paper, a combination of experimental and computational approaches is used to estimate the free energy of the interaction of Mg2+ with partially folded I state RNAs and to consider the possibility that Mg2+ favors "compaction" of the I state to a set of conformations with a higher average charge density. A sequence variant with a drastically destabilized tertiary structure was used as a mimic of I state RNA; as measured by small-angle X-ray scattering, it adopted a progressively more compact conformation over a wide Mg2+ concentration range. Average free energies of the interaction of Mg2+ with the I state mimic were obtained by a fluorescence titration method. To interpret these experimental data further, we generated molecular models of the I state and used them in calculations with the nonlinear Poisson-Boltzmarm equation to estimate the change in Mg2+-RNA interaction free energy as the average I state dimensions decrease from expanded to compact. The same models were also used to reproduce quantitatively the experimental difference in excess Mg2+ between N and I states. On the basis of these experiments and calculations, I state compaction appears to enhance Mg2+-I state interaction free energies by 10-20%, but this enhancement is at most 5% of the overall Mg2+-associated stabilization free energy for this rRNA fragment.