The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA–RNA interaction predictions provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistically long and could be formed (in three dimensions) only by going through highly entangled intermediates. Here, we present a computational pipeline to assess whether a proposed secondary (2D) structure interaction is sterically feasible and reachable along a plausible folding pathway. To this end, we simulate the folding of a series of 3D structures along a given 2D folding path. To avoid the complexity of large-scale atomic resolution simulations, our pipeline uses coarse-grained 3D modeling and breaks up the folding path into small steps, each corresponding to the extension of the interaction by 1 or 2 bp. We apply our pipeline to analyze RNA–RNA interaction formation for three selected RNA–RNA complexes. We find that kissing hairpins, in contrast to interactions in the exterior loop, are difficult to extend and tend to get stuck at an interaction length of 6 bp. Our tool, including source code, documentation, and sample data, is available at www.github.com/irenekb/RRI-3D.

中文翻译：

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通过逐步折叠模拟 2D RNA-RNA 相互作用路径的 3D 可行性

RNA 的结构，尤其是它与其他 RNA 的相互作用，提供了有关其功能的有价值的信息。基于二级结构的 RNA-RNA 相互作用预测工具提供了一种快速方法来识别可能的相互作用目标和结构。然而，这些工具忽略了空间位阻对三级（3D）结构水平的影响，并且没有考虑是否存在合适的折叠路径来形成相互作用。因此，这些工具通常会预测不切实际的长相互作用，并且只能通过高度纠缠的中间体才能形成（在三个维度上）。在这里，我们提出了一个计算管道来评估所提出的二级（2D）结构相互作用在空间上是否可行并且可以沿着合理的折叠路径到达。为此，我们模拟了一系列 3D 结构沿着给定的 2D 折叠路径的折叠。为了避免大规模原子分辨率模拟的复杂性，我们的流程使用粗粒度 3D 建模，并将折叠路径分解为小步骤，每个步骤对应于相互作用的 1 或 2 bp 扩展。我们应用我们的流程来分析三种选定的 RNA-RNA 复合物的 RNA-RNA 相互作用形成。我们发现，与外环中的相互作用相比，接吻发夹很难延伸，并且往往会卡在 6 bp 的相互作用长度处。我们的工具（包括源代码、文档和示例数据）可从 www.github.com/irenekb/RRI-3D 获取。