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使用依赖RNA的ATP酶分析监测RNA依赖性ATP酶(如SF2解旋酶)的功能性RNA结合:RIG-I案例研究

Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study.

作者信息

Guo Rong, Pyle Anna Marie

机构信息

Department of Chemistry, Yale University, New Haven, CT, United States.

Department of Chemistry, Yale University, New Haven, CT, United States; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.

出版信息

Methods Enzymol. 2022;673:39-52. doi: 10.1016/bs.mie.2022.03.064. Epub 2022 Jul 21.

Abstract

The highly conserved Superfamily 1 (SF1) and Superfamily 2 (SF2) nucleic acid-dependent ATPases, are ubiquitous motor proteins with central roles in DNA and RNA metabolism (Jankowsky & Fairman, 2007). These enzymes require RNA or DNA binding to stimulate ATPase activity, and the conformational changes that result from this coupled behavior are linked to a multitude of processes that range from nucleic acid unwinding to the flipping of macromolecular switches (Pyle, 2008, 2011). Knowledge about the relative affinity of nucleic acid ligands is crucial for deducing mechanism and understanding biological function of these enzymes. Because enzymatic ATPase activity is directly coupled to RNA binding in these proteins, one can utilize their ATPase activity as a simple reporter system for monitoring functional binding of RNA or DNA to an SF1 or SF2 enzyme. In this way, one can rapidly assess the relative impact of mutations in the protein or the nucleic acid and obtain parameters that are useful for setting up more quantitative direct binding assays. Here, we describe a routine method for employing NADH-coupled enzymatic ATPase activity to obtain kinetic parameters reflecting apparent ATP and RNA binding to an SF2 helicase. First, we provide a protocol for calibrating an NADH-couple ATPase assay using the well-characterized ATPase enzyme hexokinase, which a simple ATPase enzyme that is not coupled with nucleic acid binding. We then provide a protocol for obtaining kinetic parameters (KATP, V and KRNA) for an RNA-coupled ATPase enzyme, using the double-stranded RNA binding protein RIG-I as a case-study. These approaches are designed to provide investigators with a simple, rapid method for monitoring apparent RNA association with SF2 or SF1 helicases.

摘要

高度保守的超家族1(SF1)和超家族2(SF2)核酸依赖性ATP酶是普遍存在的运动蛋白,在DNA和RNA代谢中起核心作用(扬科夫斯基和费尔曼,2007年)。这些酶需要结合RNA或DNA来刺激ATP酶活性,这种偶联行为导致的构象变化与从核酸解核酸酸解链到大分子开关翻转等众多过程相关(派尔,2008年,2011年)。了解核酸配体的相对亲和力对于推断这些酶的作用机制和理解其生物学功能至关重要。由于这些蛋白质中的酶促ATP酶活性直接与RNA结合偶联,因此可以利用它们的ATP酶活性作为一个简单的报告系统,来监测RNA或DNA与SF1或SF2酶的功能性结合。通过这种方式,可以快速评估蛋白质或核酸中突变的相对影响,并获得有助于建立更定量的直接结合测定的参数。在这里,我们描述了一种常规方法,即利用与NADH偶联的酶促ATP酶活性来获得反映ATP和RNA与SF2解旋酶表观结合的动力学参数。首先,我们提供了一个使用特征明确的ATP酶己糖激酶校准NADH偶联ATP酶测定的方案,己糖激酶是一种不与核酸结合的简单ATP酶。然后,我们以双链RNA结合蛋白RIG-I为例,提供了一个获取RNA偶联ATP酶的动力学参数(KATP、V和KRNA)的方案。这些方法旨在为研究人员提供一种简单、快速的方法,用于监测RNA与SF2或SF1解旋酶的表观结合。

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