Modeling Riboswitches: The impact of Mg2+ ions concentration on the folding of the SAM-II riboswitch.

IF 3.2 3区生物学 Q2 BIOPHYSICS

Biophysical journal Pub Date : 2025-05-05 DOI:10.1016/j.bpj.2025.04.032

Osama Alaidi

引用次数: 0

Abstract

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 Mg2+ ions stabilizes the pre-existing 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 Mg2+ ions 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 Mg2+ ions concentration.

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模拟核开关：Mg2+离子浓度对SAM-II核开关折叠的影响。

核糖开关是存在于细菌信使RNA中的调节元件，作为小分子的传感器，因此在细菌基因调控中起着至关重要的作用。SAM-II核开关是一类识别s -腺苷型蛋氨酸的核开关。先前的研究表明，Mg2+离子的存在稳定了核开关先前存在的次要状态，其结构特征是具有成核假结，导致其概率增加。在本研究中，建立了一个分析平衡模型来描述Mg2+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的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Mg2+离子浓度的函数。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biophysical journal 生物-生物物理

CiteScore

6.10

自引率

5.90%

发文量

3090

审稿时长

2 months

期刊介绍： BJ publishes original articles, letters, and perspectives on important problems in modern biophysics. The papers should be written so as to be of interest to a broad community of biophysicists. BJ welcomes experimental studies that employ quantitative physical approaches for the study of biological systems, including or spanning scales from molecule to whole organism. Experimental studies of a purely descriptive or phenomenological nature, with no theoretical or mechanistic underpinning, are not appropriate for publication in BJ. Theoretical studies should offer new insights into the understanding ofexperimental results or suggest new experimentally testable hypotheses. Articles reporting significant methodological or technological advances, which have potential to open new areas of biophysical investigation, are also suitable for publication in BJ. Papers describing improvements in accuracy or speed of existing methods or extra detail within methods described previously are not suitable for BJ.