Lu Man, Cao Zhiqiang, Xiong Luoan, Deng Hongying, Ma Kangkang, Liu Ning, Qin Yanding, Chen Shen-Bo, Chen Jun-Hu, Li Yao, Liu Yijin, Yu Zhongbo
State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Pharmacy, Nankai University, Tianjin, China.
School of Physics and Key Laboratory of Functional Polymer Materials of Ministry of Education, Nankai University, and Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.
Commun Biol. 2025 Feb 3;8(1):165. doi: 10.1038/s42003-025-07600-3.
Ribozymes, widely found in prokaryotes and eukaryotes, target nucleic acids and can be engineered as biotechnical tools or for gene regulation or immune therapy. Among them, hammerhead is the smallest and best characterized ribozyme. However, the structure and biochemical data of ribozymes have been disagreed on, making the understanding of its catalysis mechanism a longstanding issue. Particularly, the role of conformational dynamics in ribozyme catalysis remains elusive. Here, we use single-molecule magnetic tweezers to reveal a concerted catalysis mechanism of mechanical conformational selection for a mini hammerhead ribozyme against a viral RNA sequence from the SARS-CoV-2. We identify a conformational set containing five mechanical conformers of the mini ribozyme, where magnesium ions select the active one. Our results are supported by molecular dynamics simulations. Our understanding of the RNA catalytic mechanism will be beneficial for ribozyme's biotechnological applications and as potential therapeutics against RNA viruses.
核酶广泛存在于原核生物和真核生物中，作用于核酸，可被设计成生物技术工具或用于基因调控或免疫治疗。其中，锤头状核酶是最小且特征最明确的核酶。然而，关于核酶的结构和生化数据一直存在分歧，这使得对其催化机制的理解成为一个长期存在的问题。特别是，构象动力学在核酶催化中的作用仍然难以捉摸。在这里，我们使用单分子磁镊揭示了一种小型锤头状核酶针对来自严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的病毒RNA序列进行机械构象选择的协同催化机制。我们确定了一个包含小型核酶五个机械构象的构象集，其中镁离子选择了活性构象。我们的结果得到了分子动力学模拟的支持。我们对RNA催化机制的理解将有利于核酶的生物技术应用以及作为对抗RNA病毒的潜在疗法。
