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.

程序化核糖体移码对于许多病毒（包括 HIV 和 SARS 相关冠状病毒）来说是必不可少的，它可以翻译 mRNA 上的重叠阅读框，从而产生必需的病毒蛋白。由于移码调节已被证明可显着影响病毒活力，因此 RNA 移码元件 (FSE) 已成为有吸引力的抗病毒药物靶点。然而，在治疗策略取得成功之前，必须先了解移码的复杂方面。继获得 2020 年 NSF RAPID 奖后，Schlick 数学/计算生物学实验室与 Laederach 实验 RNA 小组合作，将把图论在 RNA 上的应用（RAG：RNA-As-Graphs）与生物物理研究和生物分子建模/模拟相结合，以解开谜团。 SARS-CoV-2 及相关病毒的 RNA FSE 的结构和机制。该合作研究项目将通过计算机程序开发、数据分析和生物学解释，为包括女性和少数族裔在内的学生和博士后研究员在数学、计算机科学、生物学、物理、化学和工程学方面进行跨学科培训奠定基础。学生和博士后将学习分析、处理和可视化生物数据；设计和验证模型；开发仿真算法和粗粒度模型；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，从系统发育和生物物理学的角度描述 SARS-CoV-2 FSE 的构象和结构转变。具体来说，研究人员将通过计算和实验验证 SARS-CoV-2 亲属 FSE 的 RNA 二级结构构象景观，深入了解冠状病毒 FSE 的进化路径；通过确定 SARS-CoV-2 FSE 的转换途径来探测移码机制；并通过 RAG 反向折叠和遗传算法来识别和测试实验结构改变突变，将 FSE 转化为复杂的交织图案，以阻碍移码。这种独特的方法利用新颖的数学图论工具和生物物理模型应用于冠状病毒（包括 SARS-CoV-2）中的移码元件，将对相关病毒的结构、机制和进化趋势产生重要的见解，以解释病毒结构和移码之间的关系效率/病毒活力。通过从全局图论的角度看待结构，可以比基于序列或原子的模型更容易地识别和关联模式。确定的结构、机制和结构改变突变定义了基因治疗和治疗干预的抗病毒靶标。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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