Department of Physics, Institute of Biophysics, Central China Normal University, Wuhan 430079, China.
Int J Mol Sci. 2022 Jun 21;23(13):6903. doi: 10.3390/ijms23136903.
RNA-protein complexes regulate a variety of biological functions. Thus, it is essential to explore and visualize RNA-protein structural interaction features, especially pocket interactions. In this work, we develop an easy-to-use bioinformatics resource: RPpocket. This database provides RNA-protein complex interactions based on sequence, secondary structure, and pocket topology analysis. We extracted 793 pockets from 74 non-redundant RNA-protein structures. Then, we calculated the binding- and non-binding pocket topological properties and analyzed the binding mechanism of the RNA-protein complex. The results showed that the binding pockets were more extended than the non-binding pockets. We also found that long-range forces were the main interaction for RNA-protein recognition, while short-range forces strengthened and optimized the binding. RPpocket could facilitate RNA-protein engineering for biological or medical applications.
RNA-蛋白质复合物调节多种生物学功能。因此，探索和可视化 RNA-蛋白质结构相互作用特征，特别是口袋相互作用，至关重要。在这项工作中，我们开发了一个易于使用的生物信息学资源：RPpocket。该数据库基于序列、二级结构和口袋拓扑分析提供 RNA-蛋白质复合物相互作用。我们从 74 个非冗余 RNA-蛋白质结构中提取了 793 个口袋。然后，我们计算了结合和非结合口袋的拓扑性质，并分析了 RNA-蛋白质复合物的结合机制。结果表明，结合口袋比非结合口袋更伸展。我们还发现，远程力是 RNA-蛋白质识别的主要相互作用，而短程力则加强和优化了结合。RPpocket 可以促进 RNA-蛋白质工程在生物或医学应用中的应用。
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