埃
纳米
灵活性(工程)
电子顺磁共振
核糖开关
比例(比率)
氟化物
材料科学
纳米技术
光电子学
物理
化学
光学
结晶学
核磁共振
核糖核酸
数学
无机化学
量子力学
非编码RNA
统计
生物化学
基因
作者
Laura Remmel,Andreas Meyer,Katrin Ackermann,Gregor Hagelüken,Marina Bennati,Bela E. Bode
标识
DOI:10.26434/chemrxiv-2024-f8czr-v2
摘要
Riboswitches control gene regulation upon external stimuli such as environmental factors or ligand binding. The fluoride sensing riboswitch from Thermotoga petrophila is a complex regulatory RNA proposed to be involved in resistance to F- cytotoxicity. The details of structure and dynamics underpinning the regulatory mechanism are currently debated. Here we demonstrate that a combination of pulsed electron paramagnetic resonance (ESR/EPR) spectroscopies, detecting distances in the angstrom to nanometre range, can probe distinct regions of conformational flexibility in this riboswitch. PELDOR (pulsed electron-electron double resonance) revealed a similar preorganisation of the sensing domain in three forms, i.e. the free aptamer, the MgII-bound apo, and the F--bound holo form. 19F ENDOR (electron-nuclear double resonance) was used to investigate the active site structure of the F--bound holo form. Distance distributions without a priori structural information were compared with in silico modelling of spin label conformations based on the crystal structure. While PELDOR, probing longer distances, revealed varying conformational flexibility of the RNA backbone, ENDOR indicated low structural heterogeneity at the ligand binding site. Overall, the combination of PELDOR and ENDOR with sub-angstrom precision gave insight into structural organisation and flexibility of a riboswitch, not easily attainable by other biophysical techniques.
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