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

研究人员假设，铁和镍等元素帮助地球上古老的生命形式进食、呼吸和执行其他生命功能。事实上，这些金属是如此重要，以至于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，代表了地球表面在45亿年来一直在变化的条件的快照。之前开发了一个名为Dragon的新软件包，用于研究地球表面数十亿年来的变化如何影响铁、镍和类似金属可能属于的岩石或矿物的种类。Drag-Phire项目将这种分析扩展到生物系统，并使用最先进的网络分析来发现金属在矿物中的行为与生物系统之间的联系。这项研究将加强对地球本身如何影响35亿年进化生命的理解。罗文大学是一个以本科为主的机构，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。生命是电动的，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因子的可用性，在深层次上受行星表面还原-氧化(Redox)条件的调节。该项目将重建保存在矿物记录中的行星氧化还原条件，并将行星氧化还原历史与蛋白质辅因子利用的起源和进化联系起来。然而，由于有限的地球化学证据保存时间，重建特定的环境氧化还原条件和催化辅助因子的电子转移途径是一个令人生畏的挑战。该项目组此前开发了一个新的用户友好的基于浏览器的交互平台和R软件包，名为“地球生物本体论网络的深度氧化还原分析”或“Dragon”，它构建了矿物及其组成元素的两方网络。在这个新项目中，Dragon的功能将被扩展，以建立“蛋白质硬件集成氧化还原进化”或“Phire”网络，直接将矿物记录中的结构和/或氧化还原类似物与包含相应金属辅因子的已知蛋白质折叠联系起来。Dragon增加的新Phire功能将使Dragon-Phire项目团队能够表征关键金属辅因子(如Fe和Ni)的矿物氧化还原化学与生物电子转移过程演变背后的核心氧化还原驱动因素之间的联系。罗文大学是一个以本科生为主的机构，该项目将为包括少数族裔和/或第一代大学生在内的10-15名本科生提供参与计算地球科学研究的机会，并参与将项目成果提供给更广泛的公众。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.