The Evolutionary Origin of Non-Equilibrium Order

该项目旨在了解动态校对的进化起源，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复制到将信息保真地传递给后代，再到免疫系统区分外来病毒蛋白和我们自己的病毒蛋白。虽然动力学校对的生物物理学已经被理解，但导致其进化的力量仍然未知。直觉和目前的理论预测，更精确的分子机器将会更慢，因为它们要花更多的时间来检查错误。然而，这些理论还没有得到验证，这个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，研究团队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中的信息的分子机器，因此它可以代代相传。这个新颖的平台将允许研究人员在一次实验中研究这台机器的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，研究小组将假设聚合酶的校对可以通过选择更快的速度而进化，即使没有选择的准确性。然后，该团队将为非平衡秩序的起源开发一个理论框架，扩展当前的模型，以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。病毒的突变速率部分是由病毒复制机制及其校对能力决定的。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期间的校对，并将突变率提高到损害病毒适应性的程度。这一结果也将在生物工程中发挥作用，在生物工程中，平衡速度和准确性对Rubisco等酶至关重要，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，它就不那么精确。然而，这项研究将决定何时更快的酶也能更准确。了解这种情况何时发生，对于为商业和医疗应用创造有用的酶非常重要。该项目还将促进我们对物理学前沿领域的理解，即非平衡动力学。虽然物理学家对被动平衡系统有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比其他可能的更有序的状态。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。跨学科的研究将培养新一代的学生熟练掌握非平衡统计力学和分子生物学技术。该项目将培养一名物理学研究生，并涉及芝加哥大学生物和生物医学科学专业的本科生，让他们接触到生物学中定量和物理导向思维的好处。为了吸引更广泛的用户，他们将开发一系列名为“在错误中茁壮成长”的演示和游戏。这些活动，类似于世界游戏，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造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部当地的K-12学生共享。该奖项由分子和细胞生物科学部/生物科学理事会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。

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.