Alaidi Osama
Biocomplexity for Research and Consulting, Cairo, Egypt.
Biophys J. 2025 Jun 17;124(12):2020-2032. doi: 10.1016/j.bpj.2025.04.032. Epub 2025 May 5.
Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches that recognizes S-adenosyl methionine. It has been previously shown that the presence of Mg ions stabilizes the preexisting minor state of the riboswitch, which is structurally characterized having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg ion concentration on the folding of the SAM-II riboswitch, thus linking RNA folding and tertiary interactions energetics to ligand binding. The model enables quantitative predictions of equilibrium folding intermediates as a function of concentration of Mg ions.
核糖开关是细菌信使核糖核酸中存在的调控元件，可作为小分子的传感器，因此在细菌基因调控中发挥着至关重要的作用。SAM-II核糖开关是一类识别S-腺苷甲硫氨酸的核糖开关。先前的研究表明，镁离子的存在会稳定核糖开关预先存在的次要状态，其结构特征是具有成核假结，从而导致其概率增加。在本研究中，开发了一个分析平衡模型来描述镁离子浓度对SAM-II核糖开关折叠的影响，从而将RNA折叠和三级相互作用能量学与配体结合联系起来。该模型能够定量预测平衡折叠中间体作为镁离子浓度的函数。
