Summary: The final portion of this thesis details efforts to engineer the binding properties and chemical reactivity of antibody fragments with noncanonical amino acids. The properties of the single chain variable fragment form of a model anti-digoxin antibody have been studied after replacement of the protein’s methionine residues with methionine analogs containing alkyne, azide, and aliphatic side chains. Experiments with antibody fragments displayed on the surface of Escherichia coli cells revealed that replacement of the methionine residues of the fragment with an analog containing an alkyne side chain reduced the fluorescence levels of cells treated with a fluorescently labeled antigen to background levels, indicating loss of binding function. Replacement of methionine with analogs containing aliphatic and azide side chains left the fluorescence of cells unchanged and reduced by a factor of 0.6, respectively. Fluorescence-activated cell sorting of libraries of cell surface-displayed antibody fragments enabled the isolation of clones functional in multiple amino acid contexts. Cells displaying variants containing alkyne, azide, and aliphatic analogs and treated with fluorescently labeled antigen were more fluorescent than cells displaying the methionine form of the parent antibody fragment by factors of roughly 1.7, 3.5, and 1.3, respectively. Furthermore, the amino acid context used during highthroughput screening experiments appears to affect the frequencies of mutations occurring at various positions within the antibody fragment construct. High-throughput sequencing revealed that populations isolated in different amino acid contexts exhibit mutational rates differing by greater than twenty percent at some residues in the protein. (Abstract shortened by UMI.).