An understanding of protein structure, function, and interaction is central to biochemistry. One angle into this topic is to engage students in considering protein domains as modules that develop form and execute function semi-independently. Here, I describe a modular guided inquiry Lesson for students with an introductory background in molecular biology and biochemistry. The Lesson enables students to further explore how we define and investigate the structure and function of protein domains in a research context. Activities focus on bioinformatic approaches and interpretation and design of experiments to investigate protein interactions. Possible extensions into wet-lab and/or research projects are also highlighted. Students from various science majors enrolled in an intermediate-level biochemistry course reported that this Lesson strengthened their ability to analyze protein sequence and structure and to understand approaches to determining protein interactions.