Molecular dynamics and free energy study of the conformational equilibria in the UUUU RNA hairpin
Molecular dynamics and free energy study of the conformational equilibria in the UUUU RNA hairpin
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DOI：
10.1021/ct6003388
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发表时间：
2007-07-01
影响因子：
5.5
通讯作者：
Cieplak, Piotr
中科院分区：
文献类型：
--
作者：
Deng, Nan-Jie;Cieplak, Piotr
进行了一系列分子动力学 (MD) 模拟，以阐明 5'-CGC(UUUU)GCG-3' 寡核苷酸发夹、双链和单链形式相对稳定性的热力学基础。根据最近的核磁共振研究，该序列在室温附近的水溶液中表现出动态构象平衡。使用分子力学-泊松玻尔兹曼表面积 (MM-PB/SA) 方法进行的自由能计算支持当温度从 276 K 增加到 300 K 时构象平衡从双链体向发夹结构的转变，这与 NMR 结果一致。我们的计算也再现了添加盐对 RNA 构象异构体相对稳定性的影响。计算出的发夹和单链形式之间平衡的 Delta H 度估计为 -23.4 kcal/mol，与实验值相当一致。我们的结果表明，构象平衡很大程度上取决于溶质熵和添加盐调节的静电相互作用。在两种不同温度下进行的发夹环模拟收敛到相同的最低能量环构象。由于U5-U6-U7碱基堆积、U4碱基与连接U6和U7的磷酸盐之间的氢键以及涉及U4和U6处的2'OH基团的氢键，该构象异构体通过有利的范德华相互作用而稳定。然而，最低能量构象异构体中四种尿苷的糖皱褶与 NMR 研究报告的不同。虽然NMR研究发现U5和U7采用C2'-endo构象，但模拟结果表明，总体而言，U5和U7采用C3'-endo构象的结构在热力学上比含有C2'-endo褶皱的结构更稳定约8 kcal/mol。基于 MM-PB/SA 方案的计算表明，尽管静电溶剂化自由能有利于 U5 和 U7 核糖的 C2'-endo 构象，但它被不太有利的分子内静电和范德华能所抵消。为了增强构象采样，在发夹环的广义 Born (GB) 连续溶剂中进行了复制交换分子动力学 (REMD) 模拟。该模拟表明，在显式溶剂模拟中观察到的稳定环结构对应于自由能最小值。它还表明，虽然 U4、U5 和 U6 糖环主要处于 C3'-endo 构象，但 U7 核糖环的糖皱褶存在相当大的变化。
A series of molecular dynamics (MD) simulations was performed to elucidate the thermodynamic basis for the relative stabilities of hairpin, duplex, and single stranded forms of the 5'-CGC(UUUU)GCG-3' oligonucleotide. According to a recent NMR study this sequence exhibits dynamic conformational equilibrium in aqueous solution in the vicinity of room temperature. Free energy calculations using the molecular mechanics-Poisson Boltzmann-surface area (MM-PB/SA) approach support a shift in the conformational equilibrium from duplex to hairpin as the temperature is increased from 276 to 300 K, in agreement with the NMR results. The effect of added salt on the relative stabilities of RNA conformers is also reproduced by our calculations. The calculated Delta H degrees for the equilibrium between hairpin and single stranded forms is estimated to be -23.4 kcal/mol, in reasonable agreement with experimental values. Our results reveal that the conformational equilibrium strongly depends on the solute entropy and the electrostatic interactions modulated by added salt. Simulations of hairpin loop conducted at two different temperatures converged to the same lowest energy loop conformation. This conformer is stabilized by favorable van der Waals interactions as a result of U5-U6-U7 base stacking, a hydrogen bond between the U4 base and the phosphate linking U6 and U7, and hydrogen bonds involving the 2'OH groups at U4 and U6. However, the sugar pucker of the four uridines in the lowest energy conformer is different from that reported by a NMR study. While the NMR study found that U5 and U7 adopt the C2'-endo conformation, the simulation results suggests that overall the structure with the U5 and U7 in the C3'-endo conformation is thermodynamically more stable than the structure containing the C2'-endo pucker by approximately 8 kcal/mol. Calculations based on the MM-PB/SA scheme show that although the electrostatic solvation free energy favors the C2'-endo conformation for the U5 and U7 riboses, it is offset by the less favorable intramolecular electrostatic and van der Waals energies. To enhance the conformational sampling, a replica exchange molecular dynamics (REMD) simulation was conducted in a generalized Born (GB) continuum solvent for the hairpin loop. This simulation indicates that the stable loop structure observed in the explicit solvent simulations corresponds to the free energy minimum. It also reveals that while the U4, U5, and U6 sugar rings are predominantly in the C3'-endo conformation, there is considerable variation in the sugar pucker of the U7 ribose ring.