Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser

التفاصيل البيبلوغرافية
العنوان: Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser
المؤلفون: Jason R. Stagno, Jienv Ding, Monalisa Swain, Yun-Xing Wang, Ping Yu
المصدر: Journal of Biomolecular Nmr
سنة النشر: 2019
مصطلحات موضوعية: 0301 basic medicine, Riboswitch, Models, Molecular, Adenine riboswitch, Aptamer, B-factor, Crystallography, X-Ray, Biochemistry, Article, 03 medical and health sciences, Bound state, Molecule, Nuclear Magnetic Resonance, Biomolecular, Spectroscopy, Messenger RNA, CPMG, 030102 biochemistry & molecular biology, Chemistry, Adenine, X-ray, Aptamers, Nucleotide, Ligand (biochemistry), 030104 developmental biology, Duplex (building), Conformational exchange, Biophysics, Nucleic Acid Conformation
الوصف: Riboswitches are structured cis-regulators mainly found in the untranslated regions of messenger RNA. The aptamer domain of a riboswitch serves as a sensor for its ligand, the binding of which triggers conformational changes that regulate the behavior of its expression platform. As a model system for understanding riboswitch structures and functions, the add adenine riboswitch has been studied extensively. However, there is a need for further investigation of the conformational dynamics of the aptamer in light of the recent real-time crystallographic study at room temperature (RT) using an X-ray free electron laser (XFEL) and femtosecond X-ray crystallography (SFX). Herein, we investigate the conformational motions of the add adenine riboswitch aptamer domain, in the presence or absence of adenine, using nuclear magnetic resonance relaxation measurements and analysis of RT atomic displacement factors (B-factors). In the absence of ligand, the P1 duplex undergoes a fast exchange where the overall molecule exhibits a motion at kex ~ 319 s−1, based on imino signals. In the presence of ligand, the P1 duplex adopts a highly ordered conformation, with kex~ 83 s−1, similar to the global motion of the molecule, excluding the loops and binding pocket, at 84 s−1. The µs–ms motions in both the apo and bound states are consistent with RT B-factors. Reduced spatial atomic fluctuation, ~ 50%, in P1 upon ligand binding coincides with significantly attenuated temporal dynamic exchanges. The binding pocket is structured in the absence or presence of ligand, as evidenced by relatively low and similar RT B-factors. Therefore, despite the dramatic rearrangement of the binding pocket, those residues exhibit similar spatial thermal fluctuation before and after binding.
تدمد: 1573-5001
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e1527433a8c0a6de6f8387f240a1764e
https://pubmed.ncbi.nlm.nih.gov/31606878
حقوق: OPEN
رقم الأكسشن: edsair.doi.dedup.....e1527433a8c0a6de6f8387f240a1764e
قاعدة البيانات: OpenAIRE