The Evolutionary Origin of Non-Equilibrium Order

University Of Chicago, Chicago IL

Investigators

Abstract

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.