Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
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DOI：
10.1371/journal.pcbi.1006642
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发表时间：
2018-12-01
影响因子：
4.3
通讯作者：
Carloni, Paolo
中科院分区：
文献类型：
--
作者：
Bochicchio, Anna;Krepl, Miroslav;Carloni, Paolo
RNA识别基序（RRM）是真核生物蛋白质中最常见的RNA结合结构域。因此，设计其对任意序列的靶RNA的特异性具有重要价值。最近，Rbfox蛋白中的RRM实现了这一目标，其中设计了四个突变R118 D，E147 R，N151 S和E152 T，以靶向致癌miRNA 21的前体。在这里，我们使用了各种基于分子动力学的方法来预测结合界面处的特定相互作用。总的来说，我们已经在工程复合物和野生型Rbfox上运行了大约50微秒的增强采样和普通分子动力学模拟。pre-miRNA 20 b，从其设计突变系统。与野生型分子（蛋白质、RNA及其复合物）的可用NMR数据的比较用于建立计算的准确性。自由能计算表明，通过S151 T置换实现了亲和力和选择性的进一步改善。
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox. pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations.Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement.