Over the past decade, mechanistic cross-linking probes have been used to study protein-protein interactions in natural product biosynthetic pathways. This approach is highly interdisciplinary, combining elements of protein biochemistry, organic chemistry, and computational docking. Herein, we described the development of an experiment to engage undergraduate students in multidisciplinary research that leverages mechanistic cross-linking probes to study protein conformations and protein-protein interactions. This experiment provides students with a platform to learn chemoenzymatic synthesis, polyacrylamide gel electrophoresis, biochemical assays, and computational docking, all while exploring a contemporary biochemical topic.