College of Biological and Medical Engineering, Donghua University, Shanghai 201620, China.
National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
Biomolecules. 2024 Jun 23;14(7):742. doi: 10.3390/biom14070742.
The SAM-VI riboswitch undergoes dynamic conformational changes that modulate downstream gene expression. Traditional structural methods such as crystallography capture the bound conformation at high resolution, and additional efforts would reveal details from the dynamic transition. Here, we revealed a transcription-dependent conformation model for SAM-VI riboswitch. In this study, we combine small-angle X-ray scattering, chemical probing, and isothermal titration calorimetry to unveil the ligand-binding properties and conformational changes of the SAM-VI riboswitch and its variants. Our results suggest that the SAM-VI riboswitch contains a pre-organized ligand-binding pocket and stabilizes into the bound conformation upon binding to SAM. Whether the P1 stem formed and variations in length critically influence the conformational dynamics of the SAM-VI riboswitch. Our study provides the basis for artificially engineering the riboswitch by manipulating its peripheral sequences without modifying the SAM-binding core.
SAM-VI 核糖开关经历动态构象变化，调节下游基因表达。传统的结构方法，如晶体学，以高分辨率捕获结合构象，额外的努力将揭示动态转变的细节。在这里，我们揭示了 SAM-VI 核糖开关的转录依赖性构象模型。在这项研究中，我们结合小角度 X 射线散射、化学探测和等温滴定量热法，揭示了 SAM-VI 核糖开关及其变体的配体结合特性和构象变化。我们的结果表明，SAM-VI 核糖开关包含一个预先组织好的配体结合口袋，并在与 SAM 结合时稳定到结合构象。P1 茎的形成和长度的变化是否会对 SAM-VI 核糖开关的构象动力学产生关键影响。我们的研究为通过操纵其外围序列而不修饰 SAM 结合核心来人为工程化核糖开关提供了基础。
