CAREER: Evolutionary Principles of Intrinsically Disordered Proteins

Intrinsically disordered protein regions (IDRs) are protein regions that do not fold into a specific three-dimensional shape yet play essential roles across biology. Proteins are the workhorses of the cell. Encoded by our genes, these tiny molecules perform many key biological functions that range from converting one chemical to another to letting cells talk to each other. Historically, it was assumed that a protein needed to fold into a specific three-dimensional shape to work properly. However, over the last decade, it has become clear that certain protein regions play important roles without adopting a defined three-dimensional shape. These intrinsically disordered protein regions (IDRs) are found in around 70% of human proteins, yet because they don’t adopt a specific three-dimensional shape, they have been hard to study. One area that has been particularly challenging is understanding how disordered protein regions evolve. This is important because evolutionary information is critical for understanding how mutations impact protein function, for designing new bio-inspired materials, and for elucidating the fundamental principles of how cells work. This project will develop new computational methods to understand the types of features associated with evolutionary information in disordered proteins, as well as deploy a new way of doing accelerated artificial evolution in the lab to study how disordered regions change because of evolutionary pressure. In parallel, this project will also educate the next generation of scientists with a mixture of computational biology, machine learning, and computer science, enabling students to develop new methods to study IDRs. This project involves the development of new computational methods to identify signatures of conservation that go beyond conventional alignment-based metrics. These tools will use IDR amino acid sequence information and use it to identify signatures of evolutionary conservation in the context of molecular interactions and environmental responsiveness, taking advantage of a previously developed approach for directed evolution (OrthoRep) to evolve disordered regions under different types of selective pressure. The aim is to study how IDR sequences change under different types of evolutionary pressure if evolutionary ‘trajectories’ from the same starting point travel along similar paths in sequence space, and if trajectories from different starting points end up in the same place. The overall goal is to develop accessible methods to allow other researchers to easily analyze conservation in disordered regions, while, in parallel, expanding the foundational understanding of the biophysical and physiological constraints associated with IDR evolution. 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.