The Evolutionary Origin of Non-Equilibrium Order

该项目旨在了解动力学校正的进化起源，这是一种在消耗能量的同时提高生化准确性的机制。校对机制被认为被许多生物过程所利用，从DNA的复制到将信息忠实地传递给几代人，再到免疫系统，以区分外来病毒蛋白和我们自己的蛋白。 虽然动力学校对的生物物理学被理解，但导致其进化的力量仍然未知。直觉和当前的理论预测，更精确的分子机器会更慢，因为它们花更多的时间检查错误。然而，这些理论还没有经过测试，本项目将测试更高的精度是否意味着更高的速度或更低的速度。一些数据表明，与直觉相反，更精确的分子机器实际上可能更快。在这个奖项中，研究小组将开发一个新的实验平台来研究DNA聚合酶中这种机制的进化，DNA聚合酶是复制我们DNA中信息的分子机器，因此它可以在几代人中传播。这个新的平台将允许研究人员在一个实验中研究该机器的1000个突变体的速度和准确性。 研究小组将利用这个平台来进化DNA聚合酶，以获得更高的速度，而不需要选择更高或更低的准确性，并测量由此产生的突变率。通过这种方式，该团队将假设聚合酶中的校对可以由于更高速度的选择而进化，即使没有准确性的选择。该团队将为非平衡秩序的起源建立一个理论框架，扩展现有模型，包括记忆效应和突变熵。这项研究将对我们理解病毒和病原体的突变率如何帮助它们避开免疫系统产生重要影响。病毒必须变异以逃避人类免疫系统并繁殖，但病毒变异的速度是一把双刃剑。病毒的这种突变率部分取决于病毒的复制机制及其校正能力。 这项工作将为开发新的治疗方法提供信息，这些治疗方法针对病毒复制过程中的校对，并将突变率提高到病毒适应性受到损害的程度。这些结果在生物工程中也很有用，在生物工程中，平衡速度和准确性对于像Rubisco这样的酶至关重要，Rubisco对碳固定很重要。 人们通常认为，如果像酶这样的分子机器工作得很快，那么它的准确性就会降低。然而，这项研究将确定何时更快的酶也可以更准确。了解这种情况何时发生对于创造商业和医学应用的有用酶非常重要。该项目还将促进我们对物理学前沿领域，即非平衡动力学的理解。虽然物理学家对被动平衡系统有着深刻的理解和预测框架，但物理学家缺乏一般的理论框架来理解系统如何消耗能量并创造出比其他方式更有序的状态。该项目将揭示非平衡系统中能量成本、时间成本和精度之间的关系。跨学科研究将培养新一代精通非平衡统计力学和分子生物学技术的学生。该项目将培训一名物理学研究生，并涉及芝加哥大学生物和生物医学科学的本科生，使他们了解生物学中定量和面向物理的思维的好处。 为了接触到更广泛的受众，将开发一系列名为“在错误中茁壮成长”的演示和游戏。这些活动类似于Wordle游戏，将教授突变在病毒进化中的作用，以及定量研究如何帮助创建针对这些过程的治疗方法。这些教育资源将通过校园外展活动与芝加哥南区的当地K-12学生分享。该奖项由分子和细胞生物科学部的遗传机制和分子生物物理学项目共同资助。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的评估来支持。影响审查标准。

This project aims to understand the evolutionary origin of kinetic proofreading, a mechanism that increases biochemical accuracy while consuming energy. Proofreading mechanisms are thought to be exploited by numerous biological processes, ranging from the replication of DNA to pass information with fidelity down over generations to the immune system to distinguish foreign viral proteins from our own. While the biophysics of kinetic proofreading are understood, the forces that led to its evolution are still unknown. Intuition and current theory predicts that molecular machines that are more accurate will be slower because they spend more time checking errors. However, these theories have not been tested and this project will test whether higher accuracy implies higher speed or lower speed. Some data has suggested that counterintuitively, more accurate molecular machines might in fact be faster. In this award, the research team will develop a novel experimental platform to study the evolution of this mechanism in DNA polymerases, the molecular machines that copy information in our DNA so it can be transmitted over generations. This novel platform will allow the researchers to study the speed and accuracy of 1000s of mutants of this machine in a single experiment. The research team will exploit this platform to evolve DNA polymerases for higher speed alone, without any selection for higher or lower accuracy and measure the resulting mutation rates. In this way, the team will the hypothesis that proofreading in polymerases can evolve due to selection for higher speed, even without selection for accuracy. The team will then develop a theoretical framework for the origin of non-equilibrium order, extending current models to include memory effects and entropy of mutations.This research will have important consequences for our understanding of how mutation rates in viruses and pathogens can help them avoid the immune system. Viruses must mutate to evade the human immune system and propagate but the rate at which viruses mutate is a double-edged sword. This rate of mutations for a virus is partly determined by the viral replication machinery and its proofreading abilities. The work here will inform the development of new treatments that target proofreading during viral replication and increase mutation rates to a point where viral fitness is harmed. The results will also be useful in bioengineering, where balancing speed and accuracy is crucial for enzymes like Rubisco, which is important for carbon fixation. It is often believed that if a molecular machine like an enzyme works quickly, it is less accurate. However, this research will determine when faster enzymes can be more accurate too. Knowing when this happens is important for creating useful enzymes for commercial and medical applications.The project will also advance our understanding of a frontier region of physics, namely non-equilibrium dynamics. While physicists have a deep understanding and predictive frameworks for passive equilibrium systems, physicists lack general theoretical frameworks for understanding how systems can consume energy and create more ordered states than otherwise possible. This project will reveal relationships between energy cost, time cost and accuracy in non-equilibrium systems.The interdisciplinary research will educate a new generation of students skilled in both non-equilibrium statistical mechanics and molecular biology techniques. The project will train a physics graduate student and involving undergraduates from biological and biomedical sciences at the University of Chicago, exposing them to the benefits of quantitative and physics-oriented thinking in biology. To reach a wider audience, a series of demos and games called "Thriving through mistakes" will be developed. These activities, similar to the Wordle game, will teach about the role of mutations in virus evolution and how quantitative research can help create treatments that target these processes. These educational resources will be shared with local K-12 students on the South Side of Chicago through outreach events on campus.This award is co-funded by the Genetic Mechanisms and Molecular Biophysics programs in the Division of Molecular and Cellular Biosciences/Directorate for Biological Sciences.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.