There are over 150 currently known, highly diverse chemically modified RNAs, which are dynamic, reversible, and can modulate RNA-protein interactions. Yet, little is known about the wealth of such interactions. This can be attributed to the lack of tools that allow the rapid study of all the potential RNA modifications that might mediate RNA-protein interactions. As a promising step toward this direction, here we present a computational protocol for the characterization of interactions between proteins and RNA containing post-transcriptional modifications. Given an RNA-protein complex structure, potential RNA modified ribonucleoside positions, and molecular mechanics parameters for capturing energetics of RNA modifications, our protocol operates in two stages. In the first stage, a decision-making tool, comprising short simulations and interaction energy calculations, performs a fast and efficient search in a high-throughput fashion, through a list of different types of RNA modifications categorized into trees according to their structural and physicochemical properties, and selects a subset of RNA modifications prone to interact with the target protein. In the second stage, RNA modifications that are selected as recognized by the protein are examined in-detail using all-atom simulations and free energy calculations. We implement and experimentally validate this protocol in a test case involving the study of RNA modifications in complex with Escherichia coli (E. coli) protein Polynucleotide Phosphorylase (PNPase), depicting the favorable interaction between 8-oxo-7,8-dihydroguanosine (8-oxoG) RNA modification and PNPase. Further advancement of the protocol can broaden our understanding of protein interactions with all known RNA modifications in several systems.

中文翻译：

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“一种高通量、快速的计算方法，用于筛选可被靶蛋白识别的 RNA 转录后修饰”

目前已知的、高度多样化的化学修饰 RNA 有 150 多种，它们是动态的、可逆的，并且可以调节 RNA-蛋白质相互作用。然而，人们对这种互动的财富知之甚少。这可归因于缺乏允许快速研究可能介导 RNA-蛋白质相互作用的所有潜在 RNA 修饰的工具。作为朝着这个方向迈出的有希望的一步，我们在这里提出了一个计算协议，用于表征蛋白质和含有转录后修饰的 RNA 之间的相互作用。鉴于 RNA 蛋白质复合结构、潜在的 RNA 修饰核糖核苷位置和用于捕获 RNA 修饰能量学的分子力学参数，我们的协议分两个阶段运行。在第一阶段，决策工具，包括简短的模拟和相互作用能计算，通过根据结构和物理化学特性分类为树的不同类型的 RNA 修饰列表，以高通量方式执行快速有效的搜索，并选择易于发生的 RNA 修饰子集与目标蛋白相互作用。在第二阶段，使用全原子模拟和自由能计算详细检查被蛋白质识别的 RNA 修饰。我们在一个测试案例中实施并实验验证了该协议，该案例涉及研究与大肠杆菌 (E.coli) 蛋白多核苷酸磷酸化酶 (PNPase) 复合的 RNA 修饰，描述了 8-oxo-7,8-dihydroguanosine (8 -oxoG) RNA 修饰和 PNPase。