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.

向科罗拉多大学Anschutz医学中心颁发了奖励，以开发核磁共振（NMR）方案，以常规确定高分辨率核糖核酸（RNA）结构及其动态，仅基于经验数据，并进行适度的实验努力。尽管将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一知识不必要。该项目特别涉及RNA，但其中一些方法也会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光谱和结构生物学群落有吸引力。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性，而科学群落的重点已集中在平均结构代表上。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与结构并行评估运动至关重要的原因。因此，指导学生如何弥合这一差距是该拟议项目的关键部分，尤其是考虑到近年来大分子动力学实验的一般领域迅速发展。将招募科罗拉多大学RNA Bioscience Initiative \ Summer实习计划的暑期学生，该计划将被招募，该计划为来自有限的研究计划的机构提供了访问高级研究经验。RNA不仅是翻译遗传代码的模板进入蛋白质，但也具有多种重要的细胞功能。了解这些功能绝对取决于对原子分辨率下结构排列的知识，并且随着RNA分子的构象动力学的越来越明显。 NMR已求解了几乎一半确定的RNA结构。但是，仅凭最流行和成功的NMR探测器，即核大关增强（NOE），很少获得高分辨率RNA结构。取而代之的是，仅需要专家才能获得许多其他半经验约束和劳动密集型技术才能获得结构平均值，并且只有少数代表现实空间采样的结构的实验派生集合。因此，结构生物学群落需要新的方法来改善可以收集和用于RNA结构确定的结构数据库。原则上，NOE直接取决于两个原子之间的距离。但是，NOE被用作半定量上限距离限制。这种约束的非脱颖而出的性质意味着有关结构和动态的重要信息会丢失。我们的想法是准确测量NOE（ENOE），可以将其转换为紧密的距离极限。在理想的情况下，可以将这种距离测量至CA的准确性。 10-11米，可以在RNA分子中获得数百个质子对。这些项目提议建立一个有效的方案，以使用确切的NOE（ENOE）方法来改善各种尺寸的NMR结构，使RNA研究人员能够计算小RNA的多状态结构集合，并改善平均平均结构或特定的本地结构方面，以实现特定的局部结构方面较大的RNA。该项目的智力优点是，eNOE距离将改善所有类型的确定的NMR结构：i）可以在高分辨率的情况下定义小RNA（最多20个核苷酸）的结构，而无需任何其他限制； ENOE还可以用于计算多态结构集合以现实采样其构象空间，ii）较大的RNA分子将改善平均结构。我们将提供NMR Pulse序列代码和我们的ENOE分析程序ENORA，从我们的网页中免费下载。该协议应帮助研究人员以更高的分辨率研究RNA结构，这是更好地理解RNA功能的先决条件。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的智力优点和更广泛的影响评估的评估来支持的。

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）

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

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

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

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.

DOI：
10.1016/j.mrl.2021.10.003
发表时间：
2022-05
期刊：
Magnetic resonance letters
影响因子：
0
作者：
Born, Alexandra;Henen, Morkos A.;Nichols, Parker J.;Vogeli, Beat
通讯作者：
Vogeli, Beat

Reducing the measurement time of exact NOEs by non-uniform sampling.

DOI：
10.1007/s10858-020-00344-8
发表时间：
2020-12
期刊：
JOURNAL OF BIOMOLECULAR NMR
影响因子：
2.7
作者：
Nichols, Parker J.;Born, Alexandra;Henen, Morkos A.;Strotz, Dean;Jones, David N.;Delaglio, Frank;Vogeli, Beat
通讯作者：
Vogeli, Beat