Collaborative Research: Unraveling Structural and Mechanistic Aspects of RNA Viral Frameshifting Elements by Graph Theory and Molecular Modeling

合作研究：通过图论和分子建模揭示RNA病毒移码元件的结构和机制

• 批准号: 2151859
• 负责人: Alain Laederach
• 金额: $ 27.24万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2151859&HistoricalAwards=false
• 关键词: Collaborative; Research; Unraveling; Structural; Mechanistic

Programmed ribosomal frameshifting is indispensable to many viruses, including HIV and SARS-associated coronaviruses, to translate overlapping reading frames on the mRNA so that essential viral proteins can be produced. Because modulation of frameshifting has been shown to dramatically influence viral viability, the RNA frameshifting element (FSE) has been an attractive anti-viral drug target. However, the complex aspects of frameshifting must be understood before therapeutic strategies can succeed. Following a 2020 NSF RAPID award, the Schlick mathematics/computational biology lab, in collaboration with the Laederach experimental RNA group, will combine graph theory applications to RNA (RAG: RNA-As-Graphs) with biophysical studies and biomolecular modeling/simulation to unravel structures and mechanisms of the RNA FSE of SARS-CoV-2 and related viruses. The collaborative research program will be the basis for interdisciplinary training of students and postdoctoral fellows, including women and minorities, in mathematics, computer science, biology, physics, chemistry, and engineering, through computer program development, data analysis, and biological interpretations. Students and postdocs will learn to analyze, process, and visualize biological data; devise and validate models; develop simulation algorithms and coarse-grained models; and collect and interpret structural/functional patterns to yield new mathematical and biophysical relationships. The project will describe conformations and structural transitions of the FSE of SARS-CoV-2 from phylogenetic and biophysical viewpoints by exploiting global representation of mathematical RNA graphs. Specifically, the researchers will gain insight into the evolutionary path of the FSE of coronaviruses by computing and validating experimentally RNA secondary-structure conformational landscapes of the FSE of SARS-CoV-2 relatives; probe frameshifting mechanisms by determining the SARS-CoV-2 FSE's transition pathway; and identify and test experimentally structure-altering mutations to transform the FSE into complex intertwined motifs by RAG inverse folding and genetic algorithms to hamper frameshifting. This unique approach applied to frameshifting elements in coronaviruses including SARS-CoV-2 using novel mathematical graph-theory tools and biophysical models will yield crucial insights into the structure, mechanisms, and evolutionary trends in related viruses to explain the relationship between viral structure and frameshifting efficiency/viral viability. By looking at structure from a global graph theory point of view, patterns can be discerned and related more easily than sequence or atomic-based models. The determined structures, mechanisms, and structure-altering mutations define gene therapy and anti-viral targets for therapeutic interventions.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.

许多病毒（包括HIV和与SARS相关的冠状病毒）在MRNA上翻译重叠的阅读框，以便可以产生必需的病毒蛋白。由于已显示对帧外的调节会极大地影响病毒活力，因此RNA帧速率元件（FSE）已成为有吸引力的抗病毒药物靶标。但是，在治疗策略成功之前，必须了解框架的复杂方面。继2020年NSF快速奖之后，Schlick数学/计算生物学实验室与LAEDERACH实验RNA组合作将将图理论应用与RNA（RAG：RNA-AS-GRAPHS）与生物物理研究和生物分子模型/模拟/模拟与RNA FSARS-FSARS-COV-3的无效结构和机制相关。通过计算机程序开发，数据分析和生物学解释，该协作研究计划将是数学，计算机科学，生物学，物理学，化学和工程学的妇女和少数民族在内的学生和博士后研究员跨学科培训的基础。学生和博士后将学习分析，处理和可视化生物学数据；设计和验证模型；开发仿真算法和粗粒模型；并收集和解释结构/功能模式，以产生新的数学和生物物理关系。该项目将通过利用数学RNA图的全局表示来描述SARS-COV-2 FSE FSE的构象和结构过渡。具体而言，研究人员将通过计算和验证SARS-COV-2亲戚FSE的实验RNA二级结构构象景观来深入了解冠状病毒FSE的进化路径；通过确定SARS-COV-2 FSE的过渡途径来探测射击机制；并确定和测试实验结构改变突变，以通过碎布逆折叠和遗传算法将FSE转化为复杂的相互交织的基序，从而阻碍了Frameshifting。这种独特的方法应用于冠状病毒中的架构元素，包括使用新型的数学图理论工具和生物物理模型，将产生有关相关病毒中结构，机制和进化趋势的重要见解，以解释病毒结构与范围效率/病毒效率/病毒性/病毒性/病毒性的关系之间的关系。通过从全局图理论的角度看结构，可以比序列或基于原子的模型更容易辨别模式和更容易地关联模式。确定的结构，机制和改变结构的突变定义了治疗干预措施的基因疗法和抗病毒靶标。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影响的评估标准来评估的。

项目成果

Coordinated expression of replication-dependent histone genes from multiple loci promotes histone homeostasis in Drosophila

• DOI: 10.1091/mbc.e22-11-0532
• 发表时间: 2023-11-01
• 期刊: MOLECULAR BIOLOGY OF THE CELL
• 影响因子: 3.3
• 作者: Chaubal, Ashlesha;Waldern, Justin M.;Duronio, Robert J.
• 通讯作者: Duronio, Robert J.

Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing.

• DOI: 10.7554/elife.73888
• 发表时间: 2022-06-13
• 期刊: ELIFE
• 影响因子: 7.7
• 作者: Kumar, Jayashree;Lackey, Lela;Waldern, Justin M.;Dey, Abhishek;Mustoe, Anthony M.;Weeks, Kevin M.;Mathews, David H.;Laederach, Alain;Staley, Jonathan P.
• 通讯作者: Staley, Jonathan P.

A novel algorithm for ranking RNA structure candidates

• DOI: 10.1016/j.bpj.2021.12.004
• 发表时间: 2022-01-04
• 期刊: BIOPHYSICAL JOURNAL
• 影响因子: 3.4
• 作者: Wienecke，Anastacia;Laederach，Alain
• 通讯作者: Laederach，Alain