Learning the Shape of the Immune and Protein Universe with Armita Nourmohammad

This colloquium was originally recorded at the Aspen Center for Physics on Thursday, August 8, 2024. Our Colloquium series is for physicists, by physicists. Please see our "Public Lecture" playlists for videos intended for the general public.
The adaptive immune system consists of highly diverse B- and T-cell receptors, which can recognize a multitude of diverse pathogens. Immune recognition relies on molecular interactions between immune receptors and pathogens, which in turn is determined by the complementarity of their 3D structures and amino acid compositions, i.e., their shapes. Immune shape space has been previously introduced as an abstraction of molecular recognition in the immune system. However, the relationships between immune receptor sequence, protein structure, and specificity are very difficult to quantify in practice. In this talk, I will discuss how the growing amount of immune repertoire sequence data together with protein structures can shed light on the organization of the adaptive immune system. I will introduce physically motivated machine learning approaches to learn representations of protein micro-environments in general, and of immune receptors, in particular. The learned models reflect the relevant biophysical properties that determine a protein’s stability, and function, and could be used to predict immune recognition and to design novel immunogens e.g. for vaccine design.
Armita Nourmohammad is an Associate professor of Physics at the University of Washington, Seattle, with appointments at the Departments of Applied Mathematics, and Computer Science and Engineering. Dr. Nourmohammad works at the interface of statistical physics and biology and develops theoretical and data driven approaches to study evolutionary processes across scales. Dr. Nourmohammad obtained her Ph.D in 2012 from the University of Cologne, and then joined Princeton University as a James S. McDonnell postdoctoral fellow, where she started working on immunological problems from a biophysical and an evolutionary perspective. In 2017 Dr. Nourmohammad joined the Max Planck Society as Max Planck Research Group Leader and the University of Washington as an Assistant Professor of Physics. Dr. Nourmohammad is a recipient of an NSF CAREER award, NIH MIRA award, and the APS-DBIO Early Career Award.