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IIBR Multidisciplinary: Exact internuclear distance and dynamics measurements in RNA molecules by a novel nuclear magnetic resonance technique

IIBR 多学科：通过新型核磁共振技术精确测量 RNA 分子的核间距离和动力学

基本信息

批准号：
1917254
负责人：
Beat Vogeli
金额：
$ 48.48万
依托单位：
University of Colorado at Denver-Downtown Campus
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2019
资助国家：
美国
起止时间：
2019-10-01 至 2022-09-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1917254&HistoricalAwards=false
关键词：
IIBR Multidisciplinary Exact internuclear distance

项目摘要

An award is made to the University of Colorado Anschutz Medical Center to develop a Nuclear Magnetic Resonance (NMR) protocol to routinely determine high-resolution ribonucleic acid (RNA) structures and their dynamics based exclusively on empirical data with modest experimental effort. Although the conversion of the NMR data into interatomic distances requires in-depth understanding of the underlying physics and mathematics, the software to be developed will render this knowledge unnecessary. The project specifically concerns RNA, but some of the methods will boost the applicability to proteins as well. In combination with the anticipated reduction in measuring time, this will make the protocol attractive to the NMR spectroscopy and structural biology communities. Educationally, structural dynamics studies of RNA molecules have been largely unrepresented while the scientific communities' focus has centered on average structural representation. Macromolecules and their interactions are dynamic in nature and this is why it is critical to learn how to evaluate motions in parallel with structure. Thus, mentoring students on how to bridge this gap is a critical part of this proposed project, especially considering that the general field of macromolecular dynamics experimentation has moved quickly within recent years. A summer student from the RNA Bioscience Initiative \ Summer Internship Program at the University of Colorado will be recruited, which offers access to top-level research experience for students from institutions with limited research programs.RNA not only is the template for translating the genetic code into proteins, but also carries out diverse important cellular functions. Understanding these functions absolutely depends on knowledge of the structural arrangement at atomic resolution, and, as is becoming increasingly evident, the conformational dynamics of RNA molecules. Almost one-half of the determined RNA structures have been solved by NMR. However, high-resolution RNA structures can rarely be obtained from the most popular and successful NMR probe alone, the Nuclear Overhauser Enhancement (NOE). Instead, many additional semi-empirical restraints and labor-intensive techniques only accessible to experts are required to obtain a structural average, and there are only a few experimentally derived ensembles of structures representing realistic spatial sampling. Therefore, the structural biology community is in need of novel methods that improve the pool of structural data that can be collected and used for RNA structure determination. In principle, the NOE directly depends on the distance between two atoms. However, the NOE is employed as a semi-quantitative upper limit distance restraint. The non-exact nature of this restraint means that important information about structure and dynamics is lost. It is our idea to measure the NOE exactly (eNOE), which can be converted into a tight distance limit. In ideal cases, such a distance can be measured to an accuracy of ca. 10-11 meters and can be obtained for hundreds of proton pairs in an RNA molecule. These project proposes to establish an efficient protocol to improve NMR structures of RNA of all sizes using the exact NOE (eNOE) approach, enabling RNA researchers to calculate multi-state structural ensembles for small RNAs, and improving average structures or specific local structural aspects for larger RNAs. It is the intellectual merit of this project that the eNOE distance will improve all types of determined NMR structures: i) structures of small RNAs (up to 20 nucleotides) may be defined at high resolution without any other restraints; the eNOE can also be used to calculate multi-state structural ensembles to realistically sample their conformational space, ii) larger RNA molecules will result in improved average structures. We will offer NMR pulse sequence codes and our eNOE analysis program eNORA for free download from our webpage. This protocol should help researchers to study RNA structures at higher resolution, a prerequisite for better understanding of RNA function.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

授予科罗拉多大学安舒茨医学中心一项奖项，以开发一种核磁共振（NMR）协议，以常规确定高分辨率核糖核酸（RNA）结构及其动力学，完全基于经验数据，并进行适度的实验努力。虽然将NMR数据转换为原子间距离需要深入了解基础物理和数学，但要开发的软件将使这些知识变得不必要。该项目特别关注RNA，但其中一些方法也将提高对蛋白质的适用性。结合预期的测量时间减少，这将使该方案对NMR光谱学和结构生物学社区具有吸引力。在教育上，RNA分子的结构动力学研究在很大程度上没有代表，而科学界的焦点集中在平均结构表征上。大分子及其相互作用本质上是动态的，这就是为什么学习如何评估与结构平行的运动是至关重要的。因此，指导学生如何弥合这一差距是这个拟议项目的一个关键部分，特别是考虑到大分子动力学实验的一般领域近年来发展迅速。将招募一名来自科罗拉多大学RNA生物科学倡议\暑期实习项目的暑期学生，该项目为来自研究项目有限的机构的学生提供顶级研究经验。RNA不仅是将遗传密码翻译成蛋白质的模板，而且还执行多种重要的细胞功能。理解这些功能完全取决于原子分辨率的结构排列知识，以及越来越明显的RNA分子的构象动力学。几乎一半的RNA结构已被NMR解析。然而，高分辨率的RNA结构很少能从最流行和最成功的NMR探针单独获得，核奥弗豪泽增强（NOE）。相反，许多额外的半经验的限制和劳动密集型技术，只有访问专家需要获得一个结构的平均值，只有少数实验得出的合奏代表现实的空间采样的结构。因此，结构生物学社区需要新的方法来改善可以收集和用于RNA结构测定的结构数据库。原则上，NOE直接取决于两个原子之间的距离。然而，NOE被用作半定量上限距离约束。这种约束的非精确性质意味着丢失了有关结构和动力学的重要信息。我们的想法是精确测量NOE（eNOE），它可以转换为严格的距离限制。在理想的情况下，这样的距离可以测量到约1000的精度。10-11米，可以获得一个RNA分子中的数百个质子对。这些项目提出建立一种有效的协议，使用精确NOE（eNOE）方法来改善所有大小RNA的NMR结构，使RNA研究人员能够计算小RNA的多态结构集合，并改善较大RNA的平均结构或特定局部结构方面。该项目的智力价值在于eNOE距离将改善所有类型的确定的NMR结构：i）可以在没有任何其他限制的情况下以高分辨率定义小RNA（多达20个核苷酸）的结构; eNOE还可以用于计算多态结构系综以真实地对其构象空间进行采样，ii）较大的RNA分子将导致改善的平均结构。我们将提供NMR脉冲序列代码和我们的eNOE分析程序eNORA，供您从我们的网页免费下载。该协议应帮助研究人员研究RNA结构在更高的分辨率，更好地了解RNA的功能的先决条件。这个奖项反映了NSF的法定使命，并已被认为是值得的支持，通过评估使用基金会的知识价值和更广泛的影响审查标准。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Protein Motional Details Revealed by Complementary Structural Biology Techniques

DOI：
10.1016/j.str.2020.06.001
发表时间：
2020-09-01
期刊：
STRUCTURE
影响因子：
5.7
作者：
Grohe, Kristof;Patel, Snehal;Linser, Rasmus
通讯作者：
Linser, Rasmus

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions.

通过ADAR1的Z-RNA结合结构域在ALU和核糖体RNA中识别非CPG重复序列会诱导A-Z连接。

DOI：
10.1038/s41467-021-21039-0
发表时间：
2021-02-04
期刊：
Nature communications
影响因子：
16.6
作者：
Nichols PJ;Bevers S;Henen M;Kieft JS;Vicens Q;Vögeli B
通讯作者：
Vögeli B

Reconstruction of Coupled Intra- and Interdomain Protein Motion from Nuclear and Electron Magnetic Resonance.

DOI：
10.1021/jacs.1c06289
发表时间：
2021-10-06
期刊：
Journal of the American Chemical Society
影响因子：
15
作者：
Born A;Soetbeer J;Breitgoff F;Henen MA;Sgourakis N;Polyhach Y;Nichols PJ;Strotz D;Jeschke G;Vögeli B
通讯作者：
Vögeli B

On the use of residual dipolar couplings in multi-state structure calculation of two-domain proteins.