School of Life Science, University of Science and Technology of China Hefei, Anhui, China.
Biophys J. 2010 Feb 17;98(4):627-36. doi: 10.1016/j.bpj.2009.10.040.
RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted to be thermodynamically stable in solution. This finding is further supported by separate unrestrained CHARMM27 simulations, in which the UUCG hairpin unfolds spontaneously within 10 ns. The instability of the UUCG hairpin originates from the loop region, and propagates to the stem. The results of this study provide a molecular picture of RNA hairpin unfolding and reveal problems in the force field descriptions for the conformational energy of certain RNA hairpin.
RNA 发夹环是最丰富的二级结构元件之一，参与 RNA 折叠和蛋白质-RNA 识别。为了在原子水平上描绘 RNA 发夹折叠的自由能表面，我们使用显式溶剂中的伞状采样模拟，计算了作为末端到末端距离函数的平均力势 (PMF)。使用 AMBER ff99 和 CHARMM27 力场研究了含有四环 cUUCGg 和 cUUUUg 的两个 RNA 发夹。实验上，已知 UUCG 发夹明显比 UUUU 更稳定。在这项研究中，使用 AMBER 力场的计算对两个 RNA 发夹的折叠给出了定性正确的描述，因为计算的 PMF 证实了折叠结构的整体稳定性，并且得到的相对折叠自由能与实验结果定量一致。通过更快速的分子力学-泊松玻尔兹曼表面积方法也正确地区分了发夹的稳定性，但从该方法估计的相对自由能被高估了。自由能谱表明，天然状态盆地和展开状态平台由宽的肩部区域隔开，该区域采样具有磨损末端碱基对的各种天然样结构。计算的 PMF 缺乏预期在过渡区域附近的主要障碍，这归因于 1-D 反应坐标的限制。将 PMF 结果与使用动力学方法和粗粒模型研究的其他小 RNA 发夹进行比较。由 CHARMM27 描述的两个 RNA 发夹比由 AMBER 表示的发夹更具变形性。与 AMBER 结果相比，CHARMM27 计算的 UUUU 四环的ΔG(fold)与实验结果更一致。然而，CHARMM27 计算并不能确认实验 UUCG 结构的整体稳定性；相反，预测在溶液中扩展构象是热力学稳定的。这一发现进一步得到了单独的无约束 CHARMM27 模拟的支持，其中 UUCG 发夹在 10 ns 内自发展开。UUCG 发夹的不稳定性源于环区，并传播到茎部。这项研究的结果提供了 RNA 发夹展开的分子图像，并揭示了某些 RNA 发夹构象能的力场描述中的问题。
