In Silico Modeling of RBP47B–2′,3′-cAMP Interactions Reveals Transient Binding at RNA-Recognition Motifs

RBP47B–2′,3′-cAMP相互作用的计算机模拟揭示了RNA识别基序的瞬时结合

Sudipta Joardar (2026) In Silico Modeling of RBP47B–2′,3′-cAMP Interactions Reveals Transient Binding at RNA-Recognition Motifs Figshare

Abstract

Abstract RNA-binding protein 47B (RBP47B) is a core component of plant stress granules and plays an important role in cellular responses to abiotic stress. The small molecule 2′,3′-cyclic adenosine monophosphate (2′,3′-cAMP), generated during RNA degradation, accumulates under stress conditions and promotes stress-granule assembly through interaction with RBP47B. However, the structural basis of this interaction remains unknown.Here, we used structure prediction and molecular docking to model the interaction between Arabidopsis RBP47B and 2′,3′-cAMP. The predicted full-length RBP47B structure contains three RNA recognition motif domains and a prion-like C-terminal region. Several surface-exposed binding pockets for 2′,3′-cAMP were identified, with the most favorable site located at the interface between two RNA-binding domains. In the predicted binding mode, conserved aromatic and basic residues mediate interactions with the adenine and phosphate groups of 2′,3′-cAMP, consistent with known RNA-binding features.These results suggest that 2′,3′-cAMP binds RBP47B through a transient, low-affinity interaction at RNA-binding domain interfaces, potentially modulating RNA binding and stress-granule assembly. This study provides a structural framework for future experimental validation of metabolite-mediated regulation of stress granules in plants.

摘要：RNA结合蛋白47B (RBP47B) 是植物胁迫颗粒的核心组分，在细胞对非生物胁迫的响应中发挥重要作用。RNA降解过程中产生的小分子2′,3′-环磷酸腺苷 (2′,3′-cAMP) 在胁迫条件下积累，并通过与RBP47B相互作用促进胁迫颗粒的组装。然而，这种相互作用的结构基础尚不清楚。本文利用结构预测和分子对接技术构建了拟南芥RBP47B与2′,3′-cAMP相互作用的模型。预测的RBP47B全长结构包含三个RNA识别基序结构域和一个朊病毒样C端区域。我们鉴定了几个暴露于表面的2′,3′-cAMP结合口袋，其中最佳结合位点位于两个RNA结合结构域的界面处。在预测的结合模式下，保守的芳香族和碱性残基介导与2′,3′-cAMP的腺嘌呤和磷酸基团的相互作用，这与已知的RNA结合特征一致。这些结果表明，2′,3′-cAMP通过RNA结合域界面处的瞬时低亲和力相互作用与RBP47B结合，可能调节RNA结合和应激颗粒的组装。本研究为未来通过实验验证代谢物介导的植物应激颗粒调控提供了结构框架。

Links

https://doi.org/10.6084/m9.figshare.31955784.v1
http://dx.doi.org/10.6084/m9.figshare.31955784.v1

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