Havrila Marek, Zgarbová Marie, Jurečka Petr, Banáš Pavel, Krepl Miroslav, Otyepka Michal, Šponer Jiří
Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.
Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University , tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
J Phys Chem B. 2015 Dec 10;119(49):15176-90. doi: 10.1021/acs.jpcb.5b08876. Epub 2015 Nov 30.
We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.
我们报告了一组关于HIV-1病毒起始二聚化位点的RNA吻环复合物的广泛的显式溶剂分子动力学（MD）模拟（累计模拟时间约25微秒）。尽管通过X射线、核磁共振和MD技术进行了许多结构研究，但吻环复合物中凸起嘌呤的位置尚未得到明确解析。X射线结构一致显示未配对碱基处于凸起位置，而几项核磁共振研究则显示为内凹构象。然而，这些核磁共振研究在碱基的确切取向上相互矛盾。早期的模拟研究预测为凸起构象；然而，这一发现可能因模拟时间尺度较短而存在偏差。我们长达微秒级的模拟表明，吻环复合物的所有未配对碱基更倾向于留在吻环复合物内部。我们在现有实验数据的背景下讨论了MD结果，并认为这两种构象在生物化学上都是相关的。我们还表明，MD对这个RNA系统提供了相当令人满意的描述，这与最近关于RNA力场在较小系统（如四核苷酸和四环）中表现不佳的报道形成对比。我们对此的解释是，吻环复合物主要由广泛的沃森-克里克相互作用网络稳定，而力场对这些相互作用的描述相当好。我们测试了几组不同的水/离子参数，但它们都得出了一致的结果。然而，我们证明，最近有人建议对康奈尔等人的力场中的范德华相互作用进行修改，会因失去稳定螺旋间连接的关键堆积相互作用和过度的氢键相互作用而使对吻环复合物的描述变差。
