Improvement of the NMR structural quality for RNA and DNA

提高 RNA 和 DNA 的 NMR 结构质量

• 批准号: 537258662
• 负责人: Professor Dr. Harald Schwalbe
• 金额: --
• 依托单位: Institut für Organische Chemie und Chemische Biologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/537258662?language=en
• 关键词: Improvement; NMR; structural; quality; RNA

Nuclear Magnetic Resonance spectroscopy (NMR) is very important for the characterization of DNA and RNA, encompassing a variety of methods that offer essential insight on the structure, function, interactions and conformational dynamics of these biomolecules. Despite the eminent contribution of NMR in this field, some essential tools and approaches (which are routinely available for proteins) are still missing for nucleic acids and require further development or fine-tuning. Notably, the parametrization of forcefields used for the structure determinations of nucleic acids still lacks behind. Advancing the development in this area is therefore indispensable to elucidate more accurate and high-quality well resolved NMR structures. Such approach requires verification with well characterized RNA and DNA reference systems. Our objective is to improve the currently established methods and protocols and provide high quality data to optimize the forcefield parametrization. In this respect, we already elucidated the structure of two RNA hairpin model systems (the tetraloops UUCG and CUUG) using a wealth of structural data and incorporated optimized potentials for refinement in water. The UUCG structure is currently considered to be the gold standard for forcefield optimizations and assessment by cross-validation with other methods and empirical data. We currently investigate the structure and dynamics of additional tetraloops (GCAA, GAAG). Moreover, we provide additional suitable model targets from our current extensive investigations of elements from the genome of RNA viruses (Covid-19 and West Nile Virus) and other small DNA and RNA motifs and repeats. In our endeavor to describe the ensemble characteristic of RNA structures realistically, we studied the CUUG tetraloop system, which turned out to feature substantial dynamics despite its high thermal stability. Thus, we have recently combined NMR with molecular dynamic simulations to probe the underlying conformational landscape and provide suitable structural ensembles. In this application, we will include larger RNA and DNA molecules, G-Quadruplexes, and RNA/DNA triplexes. For their structure determination, we will gather additional global, long-range structural, orientational and dynamic restraint data and utilize 3D structure prediction and homology modeling for evaluation of the nucleic acid forcefield and improvement of tools and protocols. Moreover, we aim to include the most important and occurring RNA and DNA modifications as well as several ions and plan to employ and develop approaches for the structure calculation of conformational ensembles. These new and improved parameters and methods will be made available for the structural NMR community in established software and through implementation in our existing web-portal service for NMR structure determination. In addition, we will publish the results in suitable open source databases, journals and platforms.

核磁共振光谱（NMR）对于表征DNA和RNA非常重要，其中包括各种方法，这些方法为这些生物分子的结构，功能，相互作用和构象动力学提供了必不可少的见解。尽管NMR在该领域有明显的贡献，但核酸仍缺少一些必需的工具和方法（通常可用于蛋白质），需要进一步的开发或进行微调。值得注意的是，用于核酸结构测定的力场的参数化仍然缺乏背后。因此，在该领域的发展是必不可少的，以阐明更准确和高质量的良好解决的NMR结构。这种方法需要使用良好表征的RNA和DNA参考系统进行验证。我们的目标是改善当前建立的方法和协议，并提供高质量的数据以优化力场参数化。在这方面，我们已经阐明了使用大量结构数据的两个RNA发夹模型系统（tetraloops uucg和cuug）的结构，并结合了在水中细化的优化潜力。目前，UUCG结构被认为是通过与其他方法和经验数据交叉验证进行力场优化和评估的黄金标准。目前，我们研究了其他四环（GCAA，GAAG）的结构和动力学。此外，我们从当前对RNA病毒基因组（COVID-19和West Nile病毒）以及其他小型DNA和RNA基序和重复序列的元素进行广泛研究中提供了其他合适的模型目标。在我们努力描述RNA结构的集合特征的努力中，我们研究了Cuug Tetraloop系统，尽管其热稳定性很高，但事实证明，该系统具有实质性动力学。因此，我们最近将NMR与分子动力学模拟相结合，以探测潜在的构象景观并提供合适的结构合奏。在此应用中，我们将包括较大的RNA和DNA分子，G-四链体和RNA/DNA三链三通。为了确定其结构，我们将收集其他全局，远程结构，取向和动态的约束数据，并利用3D结构预测和同源性建模来评估核酸力场以及工具和协议的改进。此外，我们的目标是包括最重要，最重要的RNA和DNA修饰，以及几种离子，并计划采用和开发构象合奏的结构计算方法。这些新的和改进的参数和方法将用于已建立软件的结构NMR社区，并通过在我们现有的Web-portal服务中实施NMR结构确定。此外，我们将在适当的开源数据库，期刊和平台中发布结果。