Physics Colloquium – Ned Budisa

Speaker: Ned Budisa, Professor & Research Chair, Dept. of Chemistry, University of Manitoba

Expanding the Genetic Code via Directed Evolution: Tools for Biophysicists, Materials Science, and Beyond

Reprogramming the genetic code to include non-canonical amino acids (ncAAs) is a powerful tool in systems bioengineering that combines synthetic biology, chemistry, biophysics, and genome manipulation. This approach enables enhanced protein biosynthesis, deeper insights into translation, and the creation of novel functionalities and new-to-nature proteins and other foldamer-scaffolds. Expansion of the genetic code results in proteins and cells with new properties, including site-specific functionalization through various bioorthogonal chemistries.

At the heart of this endeavor are aminoacyl-tRNA synthetases (aaRS), whose modified forms – paired with cognate tRNAs – form orthogonal translation systems (OTS) for precise incorporation of ncAAs, often via amber stop codons. Directed evolution under selective pressure is used to remodel the active aaRS center to accept specific ncAAs. Traditional gene libraries focus on the first-shell residues (<6 Å) and are constrained by the transformation limits of E. coli (~10⁸–10⁹ variants), often neglecting second-shell interactions (<9 Å). To overcome this, computational enzyme design and novel wet-lab strategies are driving the evolution of effective binding pockets and cellular compatibility with exotic chemicals.

I will illustrate these approaches using (i) directed evolution of enzyme pockets, (ii) adaptive laboratory evolution of the amino acid repertoire, and (iii) genomic integration of orthogonal translation machineries for synthetic cell design.

Finally, I will provide an overview of ncAAs that are valuable for biological spectroscopy and microscopy. These site-specifically incorporated ncAAs serve as vibrational, fluorescent, EPR, or NMR probes in cellular, organismic, and in vitro contexts. Over the last two decades, their use has provided unprecedented insights into protein structure and dynamics. Bioorthogonal reactions – in particular Click Chemistry – provide powerful tools to introduce labels or mimic post-translational modifications. Applications now include capturing transient interactions, tuning protein function and generating therapeutic agents such as covalent peptides and site-specific labeled antibody conjugates.

Location: Chemistry 108
Time: 3:30PM – 5:00PM
Date: April 18th, 202