RUI - dragon-phire: Deep-time Redox Analysis of the Geobiology Ontology Network - Protein Hardware Integrates Redox Evolution

RUI - Dragon-phire：地球生物学本体网络的深度氧化还原分析 - 蛋白质硬件集成氧化还原进化

• 批准号: 2020520
• 负责人: Beth Christensen
• 金额: $ 31.92万
• 依托单位: Rowan University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2020520&HistoricalAwards=false
• 关键词: RUI; dragon; phire; Deep; time

Researchers have hypothesized that elements like iron and nickel helped ancient forms of life on Earth eat, breathe, and perform other life functions. In fact, these metals are so important, that all life on Earth continue to use them today. The same metals are also preserved in ancient rocks that represent a snapshot into conditions how the Earth surface has been changing over 4.5 billion years. A new software package called dragon was previously developed to study how changes in Earth’s surface over billions of years have impacted the kinds of rocks or minerals that iron and nickel, and similar metals, can be a part of. The dragon-phire project extends this analysis to living systems and uses state-of-the-art network analysis to discover links between how metals behave in minerals compared to biological systems. This research will enhance the understanding of how the Earth itself has influenced 3.5 billion years of evolving life. Rowan University is a Predominantly Undergraduate Institution and the project will provide unique opportunities for minority and/or first- generation college students to participate in computational geoscience research.Life is electric, and all life on Earth obtains energy from electron transfer reactions. Electron transfer processes, and the availability of critical metal cofactors used to catalyze biological electron transfer, are regulated by planetary surface reduction-oxidation (redox) conditions in deep-time. This project will reconstruct planetary redox conditions preserved in the mineral record, and link planetary redox history to the origin and evolution of protein cofactor utilization. However, due to limited geochemical evidence preserved time, reconstructing the specific environmental redox conditions and catalytic cofactors from which electron transfer pathways evolved is a daunting challenge. The project team previously developed a new user-friendly interactive browser-based platform and R software package called: “Deep-time Redox Analysis of the Geobiology Ontology Network” or “dragon”, which constructs bipartite networks of minerals and their constituent elements. In this new project dragon’s functionality will be extended to build “Protein Hardware Integrates Redox Evolution” or “phire” networks that directly link structural and/or redox analogs in the mineral record with known protein folds that incorporate corresponding metal cofactors. The new phire functionality added to dragon will allow the dragon-phire project team to characterize the connections between mineral redox chemistry of crucial metal cofactors, such as Fe and Ni, and the core redox drivers behind the evolution of biological electron transfer processes. Rowan University is a Predominantly Undergraduate Institution and the project will provide opportunities for 10-15 undergraduates, including minority and/or first- generation college students, to participate in computational geoscience research and be involved in making the project results available to the wider public.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.

研究人员假设，像铁和镍这样的元素有助于地球上古代生命的进食、呼吸和其他生命功能。事实上，这些金属非常重要，地球上的所有生命今天都在继续使用它们。同样的金属也保存在古老的岩石中，这些岩石代表了地球表面在45亿年里的变化情况。之前开发了一个名为dragon的新软件包，用于研究数十亿年来地球表面的变化如何影响铁和镍以及类似金属可能构成的岩石或矿物的种类。dragon-phire项目将这种分析扩展到生命系统，并使用最先进的网络分析来发现矿物中金属与生物系统之间的联系。这项研究将加深人们对地球本身如何影响35亿年的生命进化的理解。罗文大学是一所以本科生为主的大学，该项目将为少数族裔和/或第一代大学生提供参与计算地球科学研究的独特机会。生命是带电的，地球上所有的生命都从电子转移反应中获得能量。电子转移过程以及用于催化生物电子转移的关键金属辅助因子的可用性受行星表面深度还原-氧化（氧化还原）条件的调节。本项目将重建矿物记录中保存的行星氧化还原条件，并将行星氧化还原历史与蛋白质辅助因子利用的起源和演化联系起来。然而，由于地球化学证据保存时间有限，重建电子转移途径进化的特定环境氧化还原条件和催化辅助因子是一项艰巨的挑战。项目团队此前开发了一个新的用户友好的基于浏览器的交互式平台和R软件包，名为“深度时间氧化还原分析地球生物本体网络”或“龙”，它构建了矿物及其组成元素的两部分网络。在这个新项目中，dragon的功能将扩展到构建“蛋白质硬件集成氧化还原演化”或“phire”网络，该网络直接将矿物记录中的结构和/或氧化还原类似物与已知的包含相应金属辅因子的蛋白质折叠连接起来。添加到dragon的新phire功能将允许dragon-phire项目团队描述关键金属辅助因子（如Fe和Ni）的矿物氧化还原化学之间的联系，以及生物电子转移过程进化背后的核心氧化还原驱动因素。罗文大学是一所以本科生为主的大学，该项目将为10-15名本科生（包括少数族裔和/或第一代大学生）提供参与计算地球科学研究的机会，并参与将项目结果提供给更广泛的公众。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。