Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.
Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.
J Phys Chem B. 2019 Feb 21;123(7):1505-1511. doi: 10.1021/acs.jpcb.8b10791. Epub 2019 Feb 7.
We develop a simple, coarse-grained approach for simulating the folding of the Beet Western Yellow Virus (BWYV) pseudoknot toward the goal of creating a transferable model that can be used to study other small RNA molecules. This approach combines a structure-based model (SBM) of RNA with an electrostatic scheme that has previously been shown to correctly reproduce ionic condensation in the native basin. Mg ions are represented explicitly, directly incorporating ion-ion correlations into the system, and K is represented implicitly, through the mean-field generalized Manning counterion condensation theory. Combining the electrostatic scheme with a SBM enables the electrostatic scheme to be tested beyond the native basin. We calibrate the SBM to reproduce experimental BWYV unfolding data by eliminating overstabilizing backbone interactions from the molecular contact map and by strengthening base pairing and stacking contacts relative to other native contacts, consistent with the experimental observation that relative helical stabilities are central determinants of the RNA unfolding sequence. We find that this approach quantitatively captures the Mg dependence of the folding temperature and generates intermediate states that better approximate those revealed by experiment. Finally, we examine how our model captures Mg condensation about the BWYV pseudoknot and a U-tail variant, for which the nine 3' end nucleotides are replaced with uracils, and find our results to be consistent with experimental condensation measurements. This approach can be easily transferred to other RNA molecules by eliminating and strengthening the same classes of contacts in the SBM and including generalized Manning counterion condensation.
我们开发了一种简单的、粗粒化的方法来模拟 Beet Western Yellow 病毒（BWYV）假结向目标的折叠，旨在创建一个可转移的模型，用于研究其他小 RNA 分子。该方法将 RNA 的结构模型（SBM）与静电方案相结合，该静电方案以前被证明可以正确再现天然盆地中的离子缩合。Mg 离子被明确表示，直接将离子-离子相关性纳入系统，而 K 通过平均场广义 Manning 抗衡离子凝聚理论以隐含的方式表示。将静电方案与 SBM 结合使用，可以使静电方案在天然盆地之外得到验证。我们通过从分子接触图中消除过度稳定的骨架相互作用，并相对于其他天然相互作用增强碱基配对和堆积相互作用，使 SBM 来重现实验性 BWYV 展开数据，这与实验观察到的相对螺旋稳定性是 RNA 展开序列的中心决定因素一致。我们发现这种方法可以定量捕捉折叠温度的 Mg 依赖性，并产生更接近实验揭示的中间状态。最后，我们检查了我们的模型如何捕捉 BWYV 假结和 U-尾变体的 Mg 凝聚，其中 3'端的九个核苷酸被替换为尿嘧啶，我们的结果与实验凝聚测量结果一致。通过在 SBM 中消除和增强相同类型的相互作用，并包括广义 Manning 抗衡离子凝聚，可以将这种方法轻松转移到其他 RNA 分子上。
