The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.
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DOI：
10.1021/ct300240k
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发表时间：
2012-07-10
影响因子：
5.5
通讯作者：
Mathews, David H.
中科院分区：
文献类型：
--
作者：
Spasic, Aleksandar;Serafini, John;Mathews, David H.
研究了Amber ff99力场预测RNA螺旋形成的相对自由能的能力。测试系统是具有相同环和不同茎的三个六环RNA发夹。用伞形抽样法计算了发夹从天然状态伸展到伸展构象的平均力势。因为发夹具有相同的环序列，所以自由能变化的差异仅来自茎组成。Amber ff99力场能够正确预测发夹的稳定性顺序，尽管自由能变化的幅度大于光学熔化实验所确定的。这两种测量结果不能直接比较，因为光学熔化实验中的未折叠状态是无规线圈，而伞采样模拟中的最终状态是细长链。通过使用热力学循环，可以将计算结果与参考数据进行比较。通过使用模拟和最近邻数据将热力学循环应用于发夹之间的转变，发现一致性在模拟的抽样误差范围内，从而证明ff99力场能够准确预测RNA螺旋形成的相对自由能。
The ability of the Amber ff99 force field to predict relative free energies of RNA helix formation was investigated. The test systems were three hexaloop RNA hairpins with identical loops and varying stems. The potential of mean force of stretching the hairpins from the native state to an extended conformation was calculated with umbrella sampling. Because the hairpins have identical loop sequence, the differences in free energy changes are only from the stem composition. The Amber ff99 force field was able to correctly predict the order of stabilities of the hairpins, although the magnitude of the free energy change is larger than that determined by optical melting experiments. The two measurements cannot be compared directly because the unfolded state in the optical melting experiments is a random coil, while the end state in the umbrella sampling simulations was an elongated chain. The calculations can be compared to reference data by using a thermodynamic cycle. By applying the thermodynamic cycle to the transitions between the hairpins using simulations and nearest neighbor data, agreement was found to be within the sampling error of simulations, thus demonstrating that ff99 force field is able to accurately predict relative free energies of RNA helix formation.
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