Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study,ACS Chemical Biology

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Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study
ACS Chemical Biology ( IF 3.5 ) Pub Date : 2021-08-24 , DOI: 10.1021/acschembio.1c00417
María de Las Nieves Piña ₁ , Antonio Frontera ₁ , Antonio Bauza ₁

Affiliation

In this study, we provide experimental (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the involvement of charge assisted chalcogen bonding (ChB) interactions in the recognition and folding mechanisms of S-adenosylmethionine (SAM) riboswitches. Concretely, an initial PDB search revealed several examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine (EEM) molecules and uracil (U) bases belonging to RNA take place. While these interactions are usually described as a merely Coulombic attraction between the positively charged S/Se group and RNA, theoretical calculations indicated that the σ holes of S and Se are involved. Moreover, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader’s “Atoms in Molecules” (AIM) theory, Non-Covalent Interaction plot (NCIplot) visual index, and Natural Bonding Orbital (NBO) analyses. As far as our knowledge extends, this is the first time that ChBs in SAM–RNA complexes have been systematically analyzed, and we believe the results might be useful for scientists working in the field of RNA engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

中文翻译：

SAM 核糖开关中的电荷辅助 S/Se 硫属元素键：PDB 和 ab Initio 组合研究

在这项研究中，我们提供了实验（蛋白质数据库（PDB）检查）和理论（RI-MP2/def2-TZVP 理论水平）证据，证明电荷辅助硫属元素键合 (ChB) 相互作用参与识别和折叠机制S-腺苷甲硫氨酸 (SAM) 核糖开关。具体而言，最初的 PDB 搜索揭示了几个例子，其中 S-腺苷甲硫氨酸 (SAM)/腺苷硒甲硫氨酸 (EEM) 分子和属于 RNA 的尿嘧啶 (U) 碱基之间发生 ChB。虽然这些相互作用通常被描述为带正电的 S/Se 基团和 RNA 之间的库仑吸引力，但理论计算表明 S 和 Se 的 σ 孔也参与其中。此外，计算模型阐明了相互作用的强度和方向性，还使用巴德的“分子中的原子”（AIM）理论、非共价相互作用图（NCIplot）视觉指数和自然键合轨道（NBO）分析从电荷密度的角度进一步表征。就我们的知识范围而言，这是第一次系统地分析 SAM-RNA 复合物中的 ChB，我们相信这些结果可能对在 RNA 工程和化学生物学领域工作的科学家有用，并增加生物群落之间相互作用的可见性。

更新日期：2021-09-17

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