Yildirim Ilyas, Stern Harry A, Sponer Jiri, Spackova Nada, Turner Douglas H
Department of Physics and Astronomy, Department of Chemistry and Department of Pediatrics, University of Rochester, Rochester, New York, 14627, and Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 61265 Brno, Czech Republic.
J Chem Theory Comput. 2009 Aug 11;5(8):2088-2100. doi: 10.1021/ct800540c. Epub 2009 Jul 2.
Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5'-GCGGACGC-3')(2), (5'-GCiGGAiCGC-3')(2), (5'-GGCGAGCC-3')(2), and (5'-GGiCGAiGCC-3')(2). Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave DeltaG degrees values 2-4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of DeltaG degrees from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions.
鸟嘌呤 - 腺嘌呤（GA）碱基对在决定RNA的结构、动力学和稳定性方面起着重要作用。在RNA内部环中，GA碱基对常常串联排列，其结构取决于上下文和序列。本文所报告的计算通过将自由能差的计算预测结果与基于RNA基序（5'-GCGGACGC-3'）(2)、（5'-GCiGGAiCGC-3'）(2)、（5'-GGCGAGCC-3'）(2)和（5'-GGiCGAiGCC-3'）(2)的核磁共振（NMR）确定结构所预期的自由能差进行比较，来测试采用amber99力场的热力学积分（TI）方法。在此，iG和iC分别表示异鸟苷和异胞苷，它们相对于鸟苷和胞苷，氨基和羰基的位置互换。NMR结构表明，GA碱基对根据相邻碱基对的身份和方向，采取亚氨基（顺式沃森 - 克里克/沃森 - 克里克A - G）或剪切（反式 hoogsteen/糖边缘A - G）构象。开发了一种用于TI方法的新混合函数，该函数允许原子在初始态和终态都能消失的炼金术转变。无约束计算得到的ΔG°值与基于NMR数据的预期值相差2 - 4千卡/摩尔。用氢键约束来限制结构并没有改善预测结果。然而，当用弱位置约束来限制结构以在实验确定的NMR结构周围进行采样时，与NMR数据的一致性提高了0.7至1.5千卡/摩尔。对amber99力场进行了修改，以部分纳入亚氨基GA碱基对中鸟苷未配对氨基的锥化效应。在与实验的比较中，这几乎没有或没有带来改善。当结构具有与G氨基潜在的跨链平面外氢键时，观察到了微小的改善。使用位置约束和非平面氨基的计算重现了实验结果中ΔG°的符号，因此能够提供有用的定性见解，作为NMR实验的补充。计算中各项的分解表明，主导项来自碱基对中除氢键之外的静电和链间相互作用。结果表明，更好地描述主链是通过计算自由能预测重现实验自由能结果的关键。
